-- dump date 20140620_004533 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1427342000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1427342000002 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342000003 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1427342000004 Walker A motif; other site 1427342000005 ATP binding site [chemical binding]; other site 1427342000006 Walker B motif; other site 1427342000007 arginine finger; other site 1427342000008 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 1427342000009 DnaA box-binding interface [nucleotide binding]; other site 1427342000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 1427342000011 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 1427342000012 putative DNA binding surface [nucleotide binding]; other site 1427342000013 dimer interface [polypeptide binding]; other site 1427342000014 beta-clamp/clamp loader binding surface; other site 1427342000015 beta-clamp/translesion DNA polymerase binding surface; other site 1427342000016 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1427342000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342000018 Walker A/P-loop; other site 1427342000019 ATP binding site [chemical binding]; other site 1427342000020 Q-loop/lid; other site 1427342000021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342000022 ABC transporter signature motif; other site 1427342000023 Walker B; other site 1427342000024 D-loop; other site 1427342000025 H-loop/switch region; other site 1427342000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1427342000027 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342000028 Mg2+ binding site [ion binding]; other site 1427342000029 G-X-G motif; other site 1427342000030 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 1427342000031 anchoring element; other site 1427342000032 dimer interface [polypeptide binding]; other site 1427342000033 ATP binding site [chemical binding]; other site 1427342000034 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 1427342000035 active site 1427342000036 putative metal-binding site [ion binding]; other site 1427342000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1427342000038 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342000039 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1427342000040 putative acyl-acceptor binding pocket; other site 1427342000041 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 1427342000042 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342000043 active site 1427342000044 motif I; other site 1427342000045 motif II; other site 1427342000046 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 1427342000047 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 1427342000048 dimer interface [polypeptide binding]; other site 1427342000049 motif 1; other site 1427342000050 active site 1427342000051 motif 2; other site 1427342000052 motif 3; other site 1427342000053 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 1427342000054 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1427342000055 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 1427342000056 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1427342000057 putative acyl-acceptor binding pocket; other site 1427342000058 PilZ domain; Region: PilZ; pfam07238 1427342000059 hypothetical protein; Provisional; Region: PRK11212 1427342000060 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342000061 TPR motif; other site 1427342000062 binding surface 1427342000063 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 1427342000064 TrkA-N domain; Region: TrkA_N; pfam02254 1427342000065 TrkA-C domain; Region: TrkA_C; pfam02080 1427342000066 TrkA-N domain; Region: TrkA_N; pfam02254 1427342000067 TrkA-C domain; Region: TrkA_C; pfam02080 1427342000068 16S rRNA methyltransferase B; Provisional; Region: PRK10901 1427342000069 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 1427342000070 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342000071 S-adenosylmethionine binding site [chemical binding]; other site 1427342000072 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1427342000073 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1427342000074 putative active site [active] 1427342000075 substrate binding site [chemical binding]; other site 1427342000076 putative cosubstrate binding site; other site 1427342000077 catalytic site [active] 1427342000078 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1427342000079 substrate binding site [chemical binding]; other site 1427342000080 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 1427342000081 active site 1427342000082 catalytic residues [active] 1427342000083 metal binding site [ion binding]; metal-binding site 1427342000084 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 1427342000085 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342000086 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 1427342000087 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1427342000088 DNA protecting protein DprA; Region: dprA; TIGR00732 1427342000089 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1427342000090 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 1427342000091 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 1427342000092 NADP binding site [chemical binding]; other site 1427342000093 dimer interface [polypeptide binding]; other site 1427342000094 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 1427342000095 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1427342000096 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 1427342000097 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1427342000098 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1427342000099 shikimate binding site; other site 1427342000100 NAD(P) binding site [chemical binding]; other site 1427342000101 Zinc dependent phospholipase C (alpha toxin); Region: Zn_dep_PLPC; cd11009 1427342000102 Zn binding site [ion binding]; other site 1427342000103 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1427342000104 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1427342000105 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 1427342000106 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1427342000107 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1427342000108 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 1427342000109 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342000110 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 1427342000111 choline-sulfatase; Region: chol_sulfatase; TIGR03417 1427342000112 Sulfatase; Region: Sulfatase; cl17466 1427342000113 Choline sulfatase enzyme C terminal; Region: Choline_sulf_C; pfam12411 1427342000114 putative choline sulfate-utilization transcription factor; Region: chol_sulf_TF; TIGR03418 1427342000115 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000116 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 1427342000117 dimerization interface [polypeptide binding]; other site 1427342000118 substrate binding pocket [chemical binding]; other site 1427342000119 Dopa 4,5-dioxygenase family; Region: DOPA_dioxygen; pfam08883 1427342000120 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342000121 putative binding surface; other site 1427342000122 active site 1427342000123 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342000124 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342000125 active site 1427342000126 phosphorylation site [posttranslational modification] 1427342000127 intermolecular recognition site; other site 1427342000128 dimerization interface [polypeptide binding]; other site 1427342000129 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342000130 DNA binding residues [nucleotide binding] 1427342000131 dimerization interface [polypeptide binding]; other site 1427342000132 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 1427342000133 substrate binding site [chemical binding]; other site 1427342000134 active site 1427342000135 catalytic residues [active] 1427342000136 heterodimer interface [polypeptide binding]; other site 1427342000137 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 1427342000138 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 1427342000139 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000140 catalytic residue [active] 1427342000141 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342000142 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000143 The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; Region: PBP2_TrpI; cd08482 1427342000144 putative dimerization interface [polypeptide binding]; other site 1427342000145 putative substrate binding pocket [chemical binding]; other site 1427342000146 Dodecin; Region: Dodecin; pfam07311 1427342000147 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 1427342000148 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 1427342000149 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 1427342000150 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 1427342000151 haemagglutination activity domain; Region: Haemagg_act; pfam05860 1427342000152 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342000153 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342000154 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 1427342000155 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 1427342000156 Predicted membrane protein [Function unknown]; Region: COG3174 1427342000157 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 1427342000158 NAD+--asparagine ADP-ribosyltransferase [Signal transduction mechanisms]; Region: COG5585 1427342000159 GTPase-activating protein (GAP) domain found in bacterial cytotoxins, ExoS, SptP, and YopE. Part of protein secretion system; stimulates Rac1- dependent cytoskeletal changes that promote bacterial internalization; Region: ToxGAP; cd00219 1427342000160 switch II binding region; other site 1427342000161 Rac1 P-loop interaction site [polypeptide binding]; other site 1427342000162 GTP binding residues [chemical binding]; other site 1427342000163 switch I binding region; other site 1427342000164 ADP-ribosyltransferase exoenzyme; Region: ADPrib_exo_Tox; pfam03496 1427342000165 active site 1427342000166 conformational flexibility of ligand binding pocket; other site 1427342000167 ADP-ribosylating toxin turn-turn motif; other site 1427342000168 Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane]; Region: CsgG; COG1462 1427342000169 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 1427342000170 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4380 1427342000171 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342000172 sequence-specific DNA binding site [nucleotide binding]; other site 1427342000173 salt bridge; other site 1427342000174 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 1427342000175 active site 1427342000176 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 1427342000177 dimer interface [polypeptide binding]; other site 1427342000178 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 1427342000179 Ligand Binding Site [chemical binding]; other site 1427342000180 Molecular Tunnel; other site 1427342000181 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1427342000182 RNA 2'-phosphotransferase; Reviewed; Region: PRK00819 1427342000183 RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]; Region: KptA; COG1859 1427342000184 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3812 1427342000185 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000186 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000187 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342000188 putative effector binding pocket; other site 1427342000189 dimerization interface [polypeptide binding]; other site 1427342000190 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1427342000191 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 1427342000192 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 1427342000193 catalytic residues [active] 1427342000194 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 1427342000195 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 1427342000196 Predicted aminopeptidase [General function prediction only]; Region: COG4324 1427342000197 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 1427342000198 Eukaryotic phosphomannomutase; Region: PMM; cl17107 1427342000199 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342000200 motif II; other site 1427342000201 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1427342000202 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 1427342000203 trimer interface [polypeptide binding]; other site 1427342000204 putative metal binding site [ion binding]; other site 1427342000205 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 1427342000206 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 1427342000207 active site 1427342000208 Zn binding site [ion binding]; other site 1427342000209 Probable metal-binding protein (DUF2387); Region: DUF2387; pfam09526 1427342000210 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1427342000211 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 1427342000212 FeS/SAM binding site; other site 1427342000213 Uncharacterized conserved protein [Function unknown]; Region: COG1262 1427342000214 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 1427342000215 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1427342000216 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342000217 Walker A/P-loop; other site 1427342000218 ATP binding site [chemical binding]; other site 1427342000219 Q-loop/lid; other site 1427342000220 ABC transporter signature motif; other site 1427342000221 Walker B; other site 1427342000222 D-loop; other site 1427342000223 H-loop/switch region; other site 1427342000224 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 1427342000225 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1427342000226 active site 1427342000227 ATP binding site [chemical binding]; other site 1427342000228 substrate binding site [chemical binding]; other site 1427342000229 activation loop (A-loop); other site 1427342000230 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 1427342000231 metal ion-dependent adhesion site (MIDAS); other site 1427342000232 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 1427342000233 active site 1427342000234 Protein phosphatase 2C; Region: PP2C; pfam00481 1427342000235 Uncharacterized protein conserved in bacteria [Function unknown]; Region: SciT; COG3913 1427342000236 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 1427342000237 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 1427342000238 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 1427342000239 hypothetical protein; Provisional; Region: PRK07033 1427342000240 Type VI protein secretion system component VasF [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3455 1427342000241 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342000242 ligand binding site [chemical binding]; other site 1427342000243 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522 1427342000244 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 1427342000245 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3521 1427342000246 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 1427342000247 phosphopeptide binding site; other site 1427342000248 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 1427342000249 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 1427342000250 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 1427342000251 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3516 1427342000252 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 1427342000253 Protein of unknown function (DUF877); Region: DUF877; pfam05943 1427342000254 Protein of unknown function (DUF796); Region: DUF796; pfam05638 1427342000255 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 1427342000256 ImpE protein; Region: ImpE; pfam07024 1427342000257 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3518 1427342000258 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 1427342000259 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 1427342000260 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3520 1427342000261 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 1427342000262 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342000263 Walker A motif; other site 1427342000264 ATP binding site [chemical binding]; other site 1427342000265 Walker B motif; other site 1427342000266 arginine finger; other site 1427342000267 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342000268 Walker A motif; other site 1427342000269 ATP binding site [chemical binding]; other site 1427342000270 Walker B motif; other site 1427342000271 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1427342000272 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342000273 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342000274 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342000275 PAAR motif; Region: PAAR_motif; pfam05488 1427342000276 Uncharacterized conserved protein [Function unknown]; Region: COG5435 1427342000277 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342000278 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342000279 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342000280 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 1427342000281 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 1427342000282 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 1427342000283 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5351 1427342000284 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 1427342000285 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 1427342000286 active site 1427342000287 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 1427342000288 conserved hypothetical protein; Region: TIGR02270 1427342000289 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 1427342000290 active site clefts [active] 1427342000291 zinc binding site [ion binding]; other site 1427342000292 dimer interface [polypeptide binding]; other site 1427342000293 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 1427342000294 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1427342000295 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1427342000296 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 1427342000297 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1427342000298 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 1427342000299 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1427342000300 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342000301 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342000302 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 1427342000303 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 1427342000304 Subunit I/III interface [polypeptide binding]; other site 1427342000305 D-pathway; other site 1427342000306 Subunit I/VIIc interface [polypeptide binding]; other site 1427342000307 Subunit I/IV interface [polypeptide binding]; other site 1427342000308 Subunit I/II interface [polypeptide binding]; other site 1427342000309 Low-spin heme (heme a) binding site [chemical binding]; other site 1427342000310 Subunit I/VIIa interface [polypeptide binding]; other site 1427342000311 Subunit I/VIa interface [polypeptide binding]; other site 1427342000312 Dimer interface; other site 1427342000313 Putative water exit pathway; other site 1427342000314 Binuclear center (heme a3/CuB) [ion binding]; other site 1427342000315 K-pathway; other site 1427342000316 Subunit I/Vb interface [polypeptide binding]; other site 1427342000317 Putative proton exit pathway; other site 1427342000318 Subunit I/VIb interface; other site 1427342000319 Subunit I/VIc interface [polypeptide binding]; other site 1427342000320 Electron transfer pathway; other site 1427342000321 Subunit I/VIIIb interface [polypeptide binding]; other site 1427342000322 Subunit I/VIIb interface [polypeptide binding]; other site 1427342000323 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 1427342000324 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 1427342000325 Subunit III/VIIa interface [polypeptide binding]; other site 1427342000326 Phospholipid binding site [chemical binding]; other site 1427342000327 Subunit I/III interface [polypeptide binding]; other site 1427342000328 Subunit III/VIb interface [polypeptide binding]; other site 1427342000329 Subunit III/VIa interface; other site 1427342000330 Subunit III/Vb interface [polypeptide binding]; other site 1427342000331 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 1427342000332 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 1427342000333 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1427342000334 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1427342000335 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1427342000336 UbiA prenyltransferase family; Region: UbiA; pfam01040 1427342000337 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 1427342000338 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342000339 Cu(I) binding site [ion binding]; other site 1427342000340 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342000341 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342000342 Coenzyme A binding pocket [chemical binding]; other site 1427342000343 Predicted transcriptional regulators [Transcription]; Region: COG1733 1427342000344 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 1427342000345 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 1427342000346 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 1427342000347 putative NAD(P) binding site [chemical binding]; other site 1427342000348 active site 1427342000349 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 1427342000350 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 1427342000351 putative catalytic residue [active] 1427342000352 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK13027 1427342000353 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1427342000354 Transcriptional regulators [Transcription]; Region: FadR; COG2186 1427342000355 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342000356 DNA-binding site [nucleotide binding]; DNA binding site 1427342000357 FCD domain; Region: FCD; pfam07729 1427342000358 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342000359 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 1427342000360 DNA-binding site [nucleotide binding]; DNA binding site 1427342000361 FCD domain; Region: FCD; pfam07729 1427342000362 Aegerolysin; Region: Aegerolysin; pfam06355 1427342000363 transcriptional regulator; Provisional; Region: PRK10632 1427342000364 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000365 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342000366 putative effector binding pocket; other site 1427342000367 dimerization interface [polypeptide binding]; other site 1427342000368 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 1427342000369 Predicted transcriptional regulator [Transcription]; Region: COG3905 1427342000370 Water Stress and Hypersensitive response; Region: WHy; smart00769 1427342000371 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 1427342000372 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 1427342000373 PhnA protein; Region: PhnA; pfam03831 1427342000374 gamma-aminobutyrate permease; Region: GABAperm; TIGR01773 1427342000375 Spore germination protein; Region: Spore_permease; cl17796 1427342000376 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 1427342000377 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 1427342000378 tetrameric interface [polypeptide binding]; other site 1427342000379 NAD binding site [chemical binding]; other site 1427342000380 catalytic residues [active] 1427342000381 Cupin domain; Region: Cupin_2; cl17218 1427342000382 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 1427342000383 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342000384 inhibitor-cofactor binding pocket; inhibition site 1427342000385 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000386 catalytic residue [active] 1427342000387 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000388 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000389 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342000390 dimerization interface [polypeptide binding]; other site 1427342000391 guanine deaminase; Provisional; Region: PRK09228 1427342000392 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 1427342000393 active site 1427342000394 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 1427342000395 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 1427342000396 Walker A/P-loop; other site 1427342000397 ATP binding site [chemical binding]; other site 1427342000398 Q-loop/lid; other site 1427342000399 ABC transporter signature motif; other site 1427342000400 Walker B; other site 1427342000401 D-loop; other site 1427342000402 H-loop/switch region; other site 1427342000403 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1427342000404 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342000405 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1427342000406 TM-ABC transporter signature motif; other site 1427342000407 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342000408 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1427342000409 TM-ABC transporter signature motif; other site 1427342000410 peroxiredoxin; Region: AhpC; TIGR03137 1427342000411 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 1427342000412 dimer interface [polypeptide binding]; other site 1427342000413 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1427342000414 catalytic triad [active] 1427342000415 peroxidatic and resolving cysteines [active] 1427342000416 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 1427342000417 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 1427342000418 catalytic residue [active] 1427342000419 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 1427342000420 catalytic residues [active] 1427342000421 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342000422 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342000423 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 1427342000424 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 1427342000425 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 1427342000426 active site 1427342000427 putative substrate binding pocket [chemical binding]; other site 1427342000428 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 1427342000429 active site 1427342000430 tetramer interface [polypeptide binding]; other site 1427342000431 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]; Region: COG3613 1427342000432 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]; Region: COG3613 1427342000433 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 1427342000434 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 1427342000435 putative ligand binding site [chemical binding]; other site 1427342000436 oxidase reductase; Provisional; Region: PTZ00273 1427342000437 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 1427342000438 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342000439 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 1427342000440 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 1427342000441 active site 1427342000442 purine riboside binding site [chemical binding]; other site 1427342000443 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1427342000444 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342000445 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342000446 DNA binding residues [nucleotide binding] 1427342000447 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342000448 FecR protein; Region: FecR; pfam04773 1427342000449 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342000450 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342000451 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342000452 N-terminal plug; other site 1427342000453 ligand-binding site [chemical binding]; other site 1427342000454 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 1427342000455 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000456 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342000457 dimerization interface [polypeptide binding]; other site 1427342000458 Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_beta; cd03464 1427342000459 heterodimer interface [polypeptide binding]; other site 1427342000460 multimer interface [polypeptide binding]; other site 1427342000461 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 1427342000462 active site 1427342000463 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1427342000464 Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_alpha; cd03463 1427342000465 heterodimer interface [polypeptide binding]; other site 1427342000466 active site 1427342000467 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 1427342000468 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 1427342000469 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342000470 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342000471 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342000472 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342000473 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342000474 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342000475 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342000476 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1427342000477 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000478 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000479 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342000480 putative effector binding pocket; other site 1427342000481 dimerization interface [polypeptide binding]; other site 1427342000482 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342000483 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342000484 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342000485 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342000486 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 1427342000487 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 1427342000488 Nucleoside-binding outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: Tsx; COG3248 1427342000489 xanthine permease; Region: pbuX; TIGR03173 1427342000490 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342000491 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 1427342000492 Uncharacterized conserved protein [Function unknown]; Region: COG1739 1427342000493 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 1427342000494 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 1427342000495 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342000496 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342000497 metal binding site [ion binding]; metal-binding site 1427342000498 active site 1427342000499 I-site; other site 1427342000500 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 1427342000501 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342000502 dimerization interface [polypeptide binding]; other site 1427342000503 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 1427342000504 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 1427342000505 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 1427342000506 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342000507 active site 1427342000508 phosphorylation site [posttranslational modification] 1427342000509 intermolecular recognition site; other site 1427342000510 dimerization interface [polypeptide binding]; other site 1427342000511 CheB methylesterase; Region: CheB_methylest; pfam01339 1427342000512 CheD chemotactic sensory transduction; Region: CheD; cl00810 1427342000513 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 1427342000514 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 1427342000515 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 1427342000516 PAS domain; Region: PAS; smart00091 1427342000517 PAS domain; Region: PAS_9; pfam13426 1427342000518 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342000519 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342000520 dimer interface [polypeptide binding]; other site 1427342000521 putative CheW interface [polypeptide binding]; other site 1427342000522 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 1427342000523 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342000524 putative binding surface; other site 1427342000525 active site 1427342000526 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1427342000527 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1427342000528 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342000529 ATP binding site [chemical binding]; other site 1427342000530 G-X-G motif; other site 1427342000531 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 1427342000532 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342000533 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342000534 active site 1427342000535 phosphorylation site [posttranslational modification] 1427342000536 intermolecular recognition site; other site 1427342000537 dimerization interface [polypeptide binding]; other site 1427342000538 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342000539 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342000540 putative CheW interface [polypeptide binding]; other site 1427342000541 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000542 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000543 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342000544 putative effector binding pocket; other site 1427342000545 dimerization interface [polypeptide binding]; other site 1427342000546 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 1427342000547 classical (c) SDRs; Region: SDR_c; cd05233 1427342000548 NAD(P) binding site [chemical binding]; other site 1427342000549 active site 1427342000550 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 1427342000551 Sulfatase; Region: Sulfatase; pfam00884 1427342000552 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1427342000553 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342000554 Walker A/P-loop; other site 1427342000555 ATP binding site [chemical binding]; other site 1427342000556 Q-loop/lid; other site 1427342000557 ABC transporter signature motif; other site 1427342000558 Walker B; other site 1427342000559 D-loop; other site 1427342000560 H-loop/switch region; other site 1427342000561 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342000562 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 1427342000563 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 1427342000564 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342000565 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 1427342000566 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 1427342000567 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342000568 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 1427342000569 substrate binding pocket [chemical binding]; other site 1427342000570 active site 1427342000571 iron coordination sites [ion binding]; other site 1427342000572 Predicted permeases [General function prediction only]; Region: COG0679 1427342000573 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342000574 PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains...; Region: PAP2_acid_phosphatase; cd03397 1427342000575 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1427342000576 active site 1427342000577 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000578 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000579 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342000580 dimerization interface [polypeptide binding]; other site 1427342000581 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342000582 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342000583 N-terminal plug; other site 1427342000584 ligand-binding site [chemical binding]; other site 1427342000585 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342000586 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 1427342000587 active site 1427342000588 iron coordination sites [ion binding]; other site 1427342000589 substrate binding pocket [chemical binding]; other site 1427342000590 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342000591 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 1427342000592 active site 1427342000593 iron coordination sites [ion binding]; other site 1427342000594 substrate binding pocket [chemical binding]; other site 1427342000595 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1427342000596 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1427342000597 ligand binding site [chemical binding]; other site 1427342000598 homodimer interface [polypeptide binding]; other site 1427342000599 NAD(P) binding site [chemical binding]; other site 1427342000600 trimer interface B [polypeptide binding]; other site 1427342000601 trimer interface A [polypeptide binding]; other site 1427342000602 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1427342000603 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1427342000604 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1427342000605 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1427342000606 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1427342000607 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1427342000608 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1427342000609 TolR protein; Region: tolR; TIGR02801 1427342000610 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 1427342000611 Serine hydrolase; Region: Ser_hydrolase; pfam06821 1427342000612 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 1427342000613 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 1427342000614 Coenzyme A transferase; Region: CoA_trans; cl17247 1427342000615 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 1427342000616 triphosphoribosyl-dephospho-CoA synthase; Validated; Region: PRK01237 1427342000617 malonate decarboxylase subunit delta; Provisional; Region: PRK01220 1427342000618 Acetyl-CoA carboxylase beta subunit [Lipid metabolism]; Region: AccD; COG0777 1427342000619 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 1427342000620 Malonate decarboxylase gamma subunit (MdcE); Region: MdcE; pfam06833 1427342000621 phosphoribosyl-dephospho-CoA transferase; Provisional; Region: PRK01293 1427342000622 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 1427342000623 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1427342000624 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 1427342000625 Malonate transporter MadL subunit; Region: MadL; cl04273 1427342000626 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 1427342000627 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000628 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000629 The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; Region: PBP2_MdcR; cd08416 1427342000630 putative dimerization interface [polypeptide binding]; other site 1427342000631 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000632 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000633 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 1427342000634 putative substrate binding pocket [chemical binding]; other site 1427342000635 dimerization interface [polypeptide binding]; other site 1427342000636 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342000637 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 1427342000638 NAD(P) binding site [chemical binding]; other site 1427342000639 catalytic residues [active] 1427342000640 amino acid transporter; Region: 2A0306; TIGR00909 1427342000641 putative aminotransferase; Provisional; Region: PRK12403 1427342000642 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342000643 inhibitor-cofactor binding pocket; inhibition site 1427342000644 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000645 catalytic residue [active] 1427342000646 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342000647 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342000648 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 1427342000649 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 1427342000650 inhibitor site; inhibition site 1427342000651 active site 1427342000652 dimer interface [polypeptide binding]; other site 1427342000653 catalytic residue [active] 1427342000654 class II aldolase/adducin domain protein; Provisional; Region: PRK07090 1427342000655 intersubunit interface [polypeptide binding]; other site 1427342000656 active site 1427342000657 Zn2+ binding site [ion binding]; other site 1427342000658 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1427342000659 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342000660 sequence-specific DNA binding site [nucleotide binding]; other site 1427342000661 salt bridge; other site 1427342000662 Cupin domain; Region: Cupin_2; pfam07883 1427342000663 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1427342000664 Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit [Lipid metabolism]; Region: AtoA; COG2057 1427342000665 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 1427342000666 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342000667 dimer interface [polypeptide binding]; other site 1427342000668 active site 1427342000669 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 1427342000670 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000671 putative substrate translocation pore; other site 1427342000672 3-carboxy-cis,cis-muconate cycloisomerase; Provisional; Region: PRK09053 1427342000673 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 1427342000674 tetramer interface [polypeptide binding]; other site 1427342000675 active site 1427342000676 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 1427342000677 4-carboxymuconolactone decarboxylase; Region: decarb_PcaC; TIGR02425 1427342000678 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000679 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000680 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342000681 dimerization interface [polypeptide binding]; other site 1427342000682 benzoate transport; Region: 2A0115; TIGR00895 1427342000683 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000684 putative substrate translocation pore; other site 1427342000685 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000686 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342000687 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 1427342000688 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342000689 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1427342000690 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1427342000691 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 1427342000692 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1427342000693 EamA-like transporter family; Region: EamA; pfam00892 1427342000694 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342000695 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000696 D-galactonate transporter; Region: 2A0114; TIGR00893 1427342000697 putative substrate translocation pore; other site 1427342000698 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 1427342000699 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 1427342000700 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 1427342000701 dimer interface [polypeptide binding]; other site 1427342000702 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 1427342000703 active site 1427342000704 Fe binding site [ion binding]; other site 1427342000705 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342000706 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342000707 shikimate 5-dehydrogenase; Reviewed; Region: PRK12549 1427342000708 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1427342000709 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1427342000710 shikimate binding site; other site 1427342000711 NAD(P) binding site [chemical binding]; other site 1427342000712 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 1427342000713 Dehydroquinase class II; Region: DHquinase_II; pfam01220 1427342000714 active site 1427342000715 trimer interface [polypeptide binding]; other site 1427342000716 dimer interface [polypeptide binding]; other site 1427342000717 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000718 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342000719 putative substrate translocation pore; other site 1427342000720 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000721 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 1427342000722 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342000723 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342000724 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342000725 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342000726 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342000727 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342000728 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342000729 Coenzyme A binding pocket [chemical binding]; other site 1427342000730 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 1427342000731 FOG: CBS domain [General function prediction only]; Region: COG0517 1427342000732 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 1427342000733 MarR family; Region: MarR_2; cl17246 1427342000734 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1427342000735 Predicted membrane protein [Function unknown]; Region: COG3619 1427342000736 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342000737 HTH-like domain; Region: HTH_21; pfam13276 1427342000738 Integrase core domain; Region: rve; pfam00665 1427342000739 Integrase core domain; Region: rve_3; pfam13683 1427342000740 Transposase; Region: HTH_Tnp_1; pfam01527 1427342000741 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 1427342000742 Protein of unknown function (DUF2875); Region: DUF2875; pfam11394 1427342000743 Protein of unknown function (DUF3274); Region: DUF3274; pfam11678 1427342000744 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 1427342000745 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342000746 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342000747 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 1427342000748 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 1427342000749 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 1427342000750 succinate-semialdehyde dehydrogenase I; Provisional; Region: gabD; PRK11241 1427342000751 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1427342000752 tetramerization interface [polypeptide binding]; other site 1427342000753 NAD(P) binding site [chemical binding]; other site 1427342000754 catalytic residues [active] 1427342000755 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 1427342000756 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342000757 inhibitor-cofactor binding pocket; inhibition site 1427342000758 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000759 catalytic residue [active] 1427342000760 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342000761 active site 1427342000762 phosphorylation site [posttranslational modification] 1427342000763 intermolecular recognition site; other site 1427342000764 dimerization interface [polypeptide binding]; other site 1427342000765 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 1427342000766 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342000767 DNA-binding site [nucleotide binding]; DNA binding site 1427342000768 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342000769 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342000770 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000771 homodimer interface [polypeptide binding]; other site 1427342000772 catalytic residue [active] 1427342000773 Uncharacterized conserved protein [Function unknown]; Region: COG2128 1427342000774 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 1427342000775 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1427342000776 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342000777 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000778 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000779 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 1427342000780 substrate binding pocket [chemical binding]; other site 1427342000781 dimerization interface [polypeptide binding]; other site 1427342000782 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 1427342000783 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342000784 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342000785 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1427342000786 ligand binding site [chemical binding]; other site 1427342000787 flexible hinge region; other site 1427342000788 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 1427342000789 Predicted membrane protein [Function unknown]; Region: COG4539 1427342000790 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 1427342000791 Predicted permeases [General function prediction only]; Region: COG0730 1427342000792 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342000793 dimerization interface [polypeptide binding]; other site 1427342000794 putative DNA binding site [nucleotide binding]; other site 1427342000795 putative Zn2+ binding site [ion binding]; other site 1427342000796 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 1427342000797 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 1427342000798 Walker A/P-loop; other site 1427342000799 ATP binding site [chemical binding]; other site 1427342000800 Q-loop/lid; other site 1427342000801 ABC transporter signature motif; other site 1427342000802 Walker B; other site 1427342000803 D-loop; other site 1427342000804 H-loop/switch region; other site 1427342000805 TOBE-like domain; Region: TOBE_3; pfam12857 1427342000806 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 1427342000807 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000808 dimer interface [polypeptide binding]; other site 1427342000809 conserved gate region; other site 1427342000810 putative PBP binding loops; other site 1427342000811 ABC-ATPase subunit interface; other site 1427342000812 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 1427342000813 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000814 dimer interface [polypeptide binding]; other site 1427342000815 conserved gate region; other site 1427342000816 putative PBP binding loops; other site 1427342000817 ABC-ATPase subunit interface; other site 1427342000818 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 1427342000819 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 1427342000820 Uncharacterized small protein [Function unknown]; Region: COG5583 1427342000821 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342000822 PAS fold; Region: PAS_3; pfam08447 1427342000823 putative active site [active] 1427342000824 heme pocket [chemical binding]; other site 1427342000825 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342000826 PAS domain; Region: PAS_9; pfam13426 1427342000827 putative active site [active] 1427342000828 heme pocket [chemical binding]; other site 1427342000829 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342000830 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342000831 metal binding site [ion binding]; metal-binding site 1427342000832 active site 1427342000833 I-site; other site 1427342000834 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342000835 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1427342000836 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1427342000837 Di-iron ligands [ion binding]; other site 1427342000838 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1427342000839 Transposase; Region: DDE_Tnp_ISL3; pfam01610 1427342000840 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u3; cd11479 1427342000841 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1427342000842 Na binding site [ion binding]; other site 1427342000843 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 1427342000844 agmatinase; Region: agmatinase; TIGR01230 1427342000845 oligomer interface [polypeptide binding]; other site 1427342000846 putative active site [active] 1427342000847 Mn binding site [ion binding]; other site 1427342000848 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342000849 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342000850 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342000851 dimerization interface [polypeptide binding]; other site 1427342000852 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342000853 PAS fold; Region: PAS_3; pfam08447 1427342000854 putative active site [active] 1427342000855 heme pocket [chemical binding]; other site 1427342000856 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342000857 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342000858 metal binding site [ion binding]; metal-binding site 1427342000859 active site 1427342000860 I-site; other site 1427342000861 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342000862 agmatine deiminase; Provisional; Region: PRK13551 1427342000863 agmatine deiminase; Region: agmatine_aguA; TIGR03380 1427342000864 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 1427342000865 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 1427342000866 putative active site; other site 1427342000867 catalytic triad [active] 1427342000868 putative dimer interface [polypeptide binding]; other site 1427342000869 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342000870 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342000871 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342000872 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342000873 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342000874 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 1427342000875 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342000876 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1427342000877 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1427342000878 catalytic triad [active] 1427342000879 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342000880 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342000881 putative aminotransferase; Validated; Region: PRK07480 1427342000882 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342000883 inhibitor-cofactor binding pocket; inhibition site 1427342000884 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342000885 catalytic residue [active] 1427342000886 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342000887 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342000888 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342000889 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342000890 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 1427342000891 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342000892 Walker A/P-loop; other site 1427342000893 ATP binding site [chemical binding]; other site 1427342000894 Q-loop/lid; other site 1427342000895 ABC transporter signature motif; other site 1427342000896 Walker B; other site 1427342000897 D-loop; other site 1427342000898 H-loop/switch region; other site 1427342000899 TOBE domain; Region: TOBE_2; pfam08402 1427342000900 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000901 dimer interface [polypeptide binding]; other site 1427342000902 conserved gate region; other site 1427342000903 putative PBP binding loops; other site 1427342000904 ABC-ATPase subunit interface; other site 1427342000905 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342000906 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000907 dimer interface [polypeptide binding]; other site 1427342000908 conserved gate region; other site 1427342000909 putative PBP binding loops; other site 1427342000910 ABC-ATPase subunit interface; other site 1427342000911 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 1427342000912 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 1427342000913 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 1427342000914 active site 1427342000915 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342000916 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342000917 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1427342000918 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1427342000919 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342000920 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 1427342000921 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 1427342000922 Uncharacterized conserved protein [Function unknown]; Region: COG1683 1427342000923 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342000924 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000925 dimer interface [polypeptide binding]; other site 1427342000926 conserved gate region; other site 1427342000927 putative PBP binding loops; other site 1427342000928 ABC-ATPase subunit interface; other site 1427342000929 cystine transporter subunit; Provisional; Region: PRK11260 1427342000930 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342000931 substrate binding pocket [chemical binding]; other site 1427342000932 membrane-bound complex binding site; other site 1427342000933 hinge residues; other site 1427342000934 Domain of unknown function (DUF4399); Region: DUF4399; pfam14347 1427342000935 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 1427342000936 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 1427342000937 ligand binding site [chemical binding]; other site 1427342000938 NAD binding site [chemical binding]; other site 1427342000939 tetramer interface [polypeptide binding]; other site 1427342000940 catalytic site [active] 1427342000941 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 1427342000942 L-serine binding site [chemical binding]; other site 1427342000943 ACT domain interface; other site 1427342000944 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1427342000945 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342000946 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 1427342000947 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 1427342000948 SdiA-regulated; Region: SdiA-regulated; pfam06977 1427342000949 SdiA-regulated; Region: SdiA-regulated; cd09971 1427342000950 putative active site [active] 1427342000951 Periplasmic protein with OB-fold [Function unknown]; Region: COG3111 1427342000952 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 1427342000953 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 1427342000954 active site 1427342000955 Zn binding site [ion binding]; other site 1427342000956 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342000957 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342000958 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342000959 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342000960 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000961 dimer interface [polypeptide binding]; other site 1427342000962 conserved gate region; other site 1427342000963 putative PBP binding loops; other site 1427342000964 ABC-ATPase subunit interface; other site 1427342000965 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342000966 dimer interface [polypeptide binding]; other site 1427342000967 conserved gate region; other site 1427342000968 putative PBP binding loops; other site 1427342000969 ABC-ATPase subunit interface; other site 1427342000970 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1427342000971 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342000972 Walker A/P-loop; other site 1427342000973 ATP binding site [chemical binding]; other site 1427342000974 Q-loop/lid; other site 1427342000975 ABC transporter signature motif; other site 1427342000976 Walker B; other site 1427342000977 D-loop; other site 1427342000978 H-loop/switch region; other site 1427342000979 TOBE domain; Region: TOBE_2; pfam08402 1427342000980 SdiA-regulated; Region: SdiA-regulated; pfam06977 1427342000981 SdiA-regulated; Region: SdiA-regulated; cd09971 1427342000982 putative active site [active] 1427342000983 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 1427342000984 M28 Zn-peptidases include aminopeptidases and carboxypeptidases; Region: M28; cd02690 1427342000985 metal binding site [ion binding]; metal-binding site 1427342000986 Autotransporter protein or domain, integral membrane beta-barrel involved in protein secretion [Cell motility and secretion]; Region: COG5571 1427342000987 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1427342000988 trimer interface [polypeptide binding]; other site 1427342000989 active site 1427342000990 substrate binding site [chemical binding]; other site 1427342000991 CoA binding site [chemical binding]; other site 1427342000992 Uncharacterized conserved protein [Function unknown]; Region: COG3422 1427342000993 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 1427342000994 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 1427342000995 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1427342000996 active site 1427342000997 dimer interface [polypeptide binding]; other site 1427342000998 threonine dehydratase; Reviewed; Region: PRK09224 1427342000999 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1427342001000 tetramer interface [polypeptide binding]; other site 1427342001001 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001002 catalytic residue [active] 1427342001003 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 1427342001004 putative Ile/Val binding site [chemical binding]; other site 1427342001005 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 1427342001006 putative Ile/Val binding site [chemical binding]; other site 1427342001007 Predicted integral membrane protein [Function unknown]; Region: COG5528 1427342001008 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 1427342001009 NADH(P)-binding; Region: NAD_binding_10; pfam13460 1427342001010 putative NAD(P) binding site [chemical binding]; other site 1427342001011 active site 1427342001012 DoxX-like family; Region: DoxX_3; pfam13781 1427342001013 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 1427342001014 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342001015 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342001016 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 1427342001017 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342001018 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 1427342001019 putative active site [active] 1427342001020 Ap4A binding site [chemical binding]; other site 1427342001021 nudix motif; other site 1427342001022 putative metal binding site [ion binding]; other site 1427342001023 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 1427342001024 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 1427342001025 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 1427342001026 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1427342001027 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1427342001028 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001029 PAS fold; Region: PAS_3; pfam08447 1427342001030 putative active site [active] 1427342001031 heme pocket [chemical binding]; other site 1427342001032 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342001033 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342001034 metal binding site [ion binding]; metal-binding site 1427342001035 active site 1427342001036 I-site; other site 1427342001037 Uncharacterized conserved protein [Function unknown]; Region: COG3332 1427342001038 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1427342001039 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1427342001040 thymidylate synthase; Reviewed; Region: thyA; PRK01827 1427342001041 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 1427342001042 dimerization interface [polypeptide binding]; other site 1427342001043 active site 1427342001044 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 1427342001045 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1427342001046 G1 box; other site 1427342001047 GTP/Mg2+ binding site [chemical binding]; other site 1427342001048 G2 box; other site 1427342001049 Switch I region; other site 1427342001050 G3 box; other site 1427342001051 Switch II region; other site 1427342001052 G4 box; other site 1427342001053 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 1427342001054 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 1427342001055 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 1427342001056 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 1427342001057 putative active site [active] 1427342001058 catalytic site [active] 1427342001059 putative metal binding site [ion binding]; other site 1427342001060 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1427342001061 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 1427342001062 folate binding site [chemical binding]; other site 1427342001063 NADP+ binding site [chemical binding]; other site 1427342001064 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 1427342001065 active site 1427342001066 metal binding site [ion binding]; metal-binding site 1427342001067 homotetramer interface [polypeptide binding]; other site 1427342001068 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 1427342001069 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 1427342001070 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 1427342001071 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 1427342001072 putative RNA binding site [nucleotide binding]; other site 1427342001073 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001074 S-adenosylmethionine binding site [chemical binding]; other site 1427342001075 intracellular protease, PfpI family; Region: PfpI; TIGR01382 1427342001076 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 1427342001077 proposed catalytic triad [active] 1427342001078 conserved cys residue [active] 1427342001079 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 1427342001080 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1427342001081 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1427342001082 DNA binding site [nucleotide binding] 1427342001083 catalytic residue [active] 1427342001084 H2TH interface [polypeptide binding]; other site 1427342001085 putative catalytic residues [active] 1427342001086 turnover-facilitating residue; other site 1427342001087 intercalation triad [nucleotide binding]; other site 1427342001088 8OG recognition residue [nucleotide binding]; other site 1427342001089 putative reading head residues; other site 1427342001090 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1427342001091 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1427342001092 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342001093 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 1427342001094 putative acyl-acceptor binding pocket; other site 1427342001095 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1427342001096 Sel1-like repeats; Region: SEL1; smart00671 1427342001097 Sel1-like repeats; Region: SEL1; smart00671 1427342001098 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 1427342001099 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 1427342001100 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1427342001101 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 1427342001102 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 1427342001103 active site 1427342001104 (T/H)XGH motif; other site 1427342001105 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 1427342001106 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342001107 Tat-translocated enzyme; Region: tat_substr_1; TIGR01412 1427342001108 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 1427342001109 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 1427342001110 NAD(P) binding site [chemical binding]; other site 1427342001111 catalytic residues [active] 1427342001112 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342001113 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342001114 Bacterial transcriptional repressor; Region: TetR; pfam13972 1427342001115 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342001116 Coenzyme A binding pocket [chemical binding]; other site 1427342001117 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 1427342001118 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 1427342001119 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001120 S-adenosylmethionine binding site [chemical binding]; other site 1427342001121 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1427342001122 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1427342001123 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1427342001124 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1427342001125 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1427342001126 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1427342001127 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1427342001128 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 1427342001129 P loop; other site 1427342001130 GTP binding site [chemical binding]; other site 1427342001131 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 1427342001132 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342001133 Walker A/P-loop; other site 1427342001134 ATP binding site [chemical binding]; other site 1427342001135 Q-loop/lid; other site 1427342001136 ABC transporter signature motif; other site 1427342001137 Walker B; other site 1427342001138 D-loop; other site 1427342001139 H-loop/switch region; other site 1427342001140 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 1427342001141 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 1427342001142 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1427342001143 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1427342001144 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342001145 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342001146 DNA binding residues [nucleotide binding] 1427342001147 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 1427342001148 monofunctional biosynthetic peptidoglycan transglycosylase; Region: mono_pep_trsgly; TIGR02070 1427342001149 Protein of unknown function (DUF423); Region: DUF423; pfam04241 1427342001150 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 1427342001151 thiS-thiF/thiG interaction site; other site 1427342001152 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 1427342001153 ThiS interaction site; other site 1427342001154 putative active site [active] 1427342001155 tetramer interface [polypeptide binding]; other site 1427342001156 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001157 S-adenosylmethionine binding site [chemical binding]; other site 1427342001158 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 1427342001159 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 1427342001160 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342001161 HemN family oxidoreductase; Provisional; Region: PRK05660 1427342001162 FeS/SAM binding site; other site 1427342001163 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 1427342001164 active site 1427342001165 dimerization interface [polypeptide binding]; other site 1427342001166 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 1427342001167 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342001168 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001169 S-adenosylmethionine binding site [chemical binding]; other site 1427342001170 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 1427342001171 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 1427342001172 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1427342001173 G1 box; other site 1427342001174 GTP/Mg2+ binding site [chemical binding]; other site 1427342001175 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 1427342001176 G2 box; other site 1427342001177 Switch I region; other site 1427342001178 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 1427342001179 G3 box; other site 1427342001180 Switch II region; other site 1427342001181 GTP/Mg2+ binding site [chemical binding]; other site 1427342001182 G4 box; other site 1427342001183 G5 box; other site 1427342001184 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 1427342001185 YGGT family; Region: YGGT; pfam02325 1427342001186 YGGT family; Region: YGGT; pfam02325 1427342001187 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 1427342001188 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 1427342001189 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 1427342001190 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342001191 catalytic residue [active] 1427342001192 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 1427342001193 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 1427342001194 Walker A motif; other site 1427342001195 ATP binding site [chemical binding]; other site 1427342001196 Walker B motif; other site 1427342001197 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 1427342001198 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342001199 Walker A motif; other site 1427342001200 ATP binding site [chemical binding]; other site 1427342001201 Walker B motif; other site 1427342001202 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 1427342001203 Predicted membrane protein [Function unknown]; Region: XynA; COG2314 1427342001204 TM2 domain; Region: TM2; cl00984 1427342001205 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1427342001206 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 1427342001207 dimer interface [polypeptide binding]; other site 1427342001208 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001209 catalytic residue [active] 1427342001210 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well...; Region: CBS_pair_PALP_assoc2; cd04609 1427342001211 FOG: CBS domain [General function prediction only]; Region: COG0517 1427342001212 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 1427342001213 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 1427342001214 homodimer interface [polypeptide binding]; other site 1427342001215 substrate-cofactor binding pocket; other site 1427342001216 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001217 catalytic residue [active] 1427342001218 dihydroorotase; Validated; Region: pyrC; PRK09357 1427342001219 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 1427342001220 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 1427342001221 active site 1427342001222 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 1427342001223 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1427342001224 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1427342001225 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 1427342001226 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342001227 active site 1427342001228 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 1427342001229 hypothetical protein; Validated; Region: PRK00228 1427342001230 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1427342001231 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1427342001232 glutathione synthetase; Provisional; Region: PRK05246 1427342001233 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 1427342001234 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 1427342001235 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342001236 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342001237 active site 1427342001238 phosphorylation site [posttranslational modification] 1427342001239 intermolecular recognition site; other site 1427342001240 dimerization interface [polypeptide binding]; other site 1427342001241 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342001242 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342001243 active site 1427342001244 phosphorylation site [posttranslational modification] 1427342001245 intermolecular recognition site; other site 1427342001246 dimerization interface [polypeptide binding]; other site 1427342001247 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 1427342001248 putative CheA interaction surface; other site 1427342001249 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 1427342001250 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342001251 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342001252 dimer interface [polypeptide binding]; other site 1427342001253 putative CheW interface [polypeptide binding]; other site 1427342001254 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 1427342001255 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 1427342001256 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 1427342001257 Hpt domain; Region: Hpt; pfam01627 1427342001258 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342001259 putative binding surface; other site 1427342001260 active site 1427342001261 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342001262 putative binding surface; other site 1427342001263 active site 1427342001264 Hpt domain; Region: Hpt; pfam01627 1427342001265 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342001266 putative binding surface; other site 1427342001267 active site 1427342001268 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342001269 putative binding surface; other site 1427342001270 active site 1427342001271 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342001272 putative binding surface; other site 1427342001273 active site 1427342001274 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1427342001275 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1427342001276 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342001277 ATP binding site [chemical binding]; other site 1427342001278 Mg2+ binding site [ion binding]; other site 1427342001279 G-X-G motif; other site 1427342001280 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 1427342001281 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342001282 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342001283 active site 1427342001284 phosphorylation site [posttranslational modification] 1427342001285 intermolecular recognition site; other site 1427342001286 dimerization interface [polypeptide binding]; other site 1427342001287 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 1427342001288 CheB methylesterase; Region: CheB_methylest; pfam01339 1427342001289 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 1427342001290 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342001291 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342001292 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342001293 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342001294 LysE type translocator; Region: LysE; pfam01810 1427342001295 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 1427342001296 RNA methyltransferase, RsmE family; Region: TIGR00046 1427342001297 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK07030 1427342001298 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342001299 inhibitor-cofactor binding pocket; inhibition site 1427342001300 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001301 catalytic residue [active] 1427342001302 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 1427342001303 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342001304 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1427342001305 hypothetical protein; Provisional; Region: PRK03757 1427342001306 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342001307 MarR family; Region: MarR; pfam01047 1427342001308 multidrug efflux system protein MdtE; Provisional; Region: PRK09859 1427342001309 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342001310 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342001311 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 1427342001312 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342001313 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342001314 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342001315 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 1427342001316 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342001317 ATP binding site [chemical binding]; other site 1427342001318 Mg++ binding site [ion binding]; other site 1427342001319 motif III; other site 1427342001320 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342001321 nucleotide binding region [chemical binding]; other site 1427342001322 ATP-binding site [chemical binding]; other site 1427342001323 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 1427342001324 FAD binding site [chemical binding]; other site 1427342001325 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1427342001326 HD domain; Region: HD_4; pfam13328 1427342001327 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 1427342001328 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 1427342001329 homotetramer interface [polypeptide binding]; other site 1427342001330 ligand binding site [chemical binding]; other site 1427342001331 catalytic site [active] 1427342001332 NAD binding site [chemical binding]; other site 1427342001333 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342001334 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342001335 N-terminal plug; other site 1427342001336 ligand-binding site [chemical binding]; other site 1427342001337 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 1427342001338 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342001339 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 1427342001340 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342001341 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 1427342001342 cytosine deaminase; Provisional; Region: PRK09230 1427342001343 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 1427342001344 active site 1427342001345 nucleobase-cation-symport-1 (NCS1) transporter CobB-like; solute-binding domain; Region: SLC-NCS1sbd_CobB-like; cd11484 1427342001346 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342001347 Na binding site [ion binding]; other site 1427342001348 putative substrate binding site [chemical binding]; other site 1427342001349 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 1427342001350 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 1427342001351 homodimer interface [polypeptide binding]; other site 1427342001352 active site 1427342001353 FMN binding site [chemical binding]; other site 1427342001354 substrate binding site [chemical binding]; other site 1427342001355 4Fe-4S binding domain; Region: Fer4_6; pfam12837 1427342001356 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 1427342001357 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342001358 phenylhydantoinase; Validated; Region: PRK08323 1427342001359 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 1427342001360 tetramer interface [polypeptide binding]; other site 1427342001361 active site 1427342001362 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily, YbbW-like; solute-binding domain; Region: SLC-NCS1sbd_YbbW-like; cd11485 1427342001363 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342001364 Na binding site [ion binding]; other site 1427342001365 putative substrate binding site [chemical binding]; other site 1427342001366 allantoate amidohydrolase; Reviewed; Region: PRK09290 1427342001367 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 1427342001368 active site 1427342001369 metal binding site [ion binding]; metal-binding site 1427342001370 dimer interface [polypeptide binding]; other site 1427342001371 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1427342001372 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1427342001373 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 1427342001374 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342001375 FAD binding site [chemical binding]; other site 1427342001376 substrate binding pocket [chemical binding]; other site 1427342001377 catalytic base [active] 1427342001378 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342001379 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342001380 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 1427342001381 dimerization interface [polypeptide binding]; other site 1427342001382 substrate binding pocket [chemical binding]; other site 1427342001383 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 1427342001384 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342001385 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 1427342001386 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342001387 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 1427342001388 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 1427342001389 dimer interface [polypeptide binding]; other site 1427342001390 active site residues [active] 1427342001391 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 1427342001392 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 1427342001393 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1427342001394 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342001395 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342001396 substrate binding pocket [chemical binding]; other site 1427342001397 membrane-bound complex binding site; other site 1427342001398 hinge residues; other site 1427342001399 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 1427342001400 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 1427342001401 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342001402 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 1427342001403 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342001404 ATP binding site [chemical binding]; other site 1427342001405 Mg++ binding site [ion binding]; other site 1427342001406 motif III; other site 1427342001407 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342001408 nucleotide binding region [chemical binding]; other site 1427342001409 ATP-binding site [chemical binding]; other site 1427342001410 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 1427342001411 putative RNA binding site [nucleotide binding]; other site 1427342001412 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342001413 DNA-binding site [nucleotide binding]; DNA binding site 1427342001414 RNA-binding motif; other site 1427342001415 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 1427342001416 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 1427342001417 putative transporter; Provisional; Region: PRK10504 1427342001418 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342001419 putative substrate translocation pore; other site 1427342001420 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342001421 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 1427342001422 Clp amino terminal domain; Region: Clp_N; pfam02861 1427342001423 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342001424 Walker A motif; other site 1427342001425 ATP binding site [chemical binding]; other site 1427342001426 Walker B motif; other site 1427342001427 arginine finger; other site 1427342001428 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342001429 Walker A motif; other site 1427342001430 ATP binding site [chemical binding]; other site 1427342001431 Walker B motif; other site 1427342001432 arginine finger; other site 1427342001433 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1427342001434 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 1427342001435 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342001436 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 1427342001437 putative acyl-acceptor binding pocket; other site 1427342001438 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 1427342001439 DNA-binding response regulator CreB; Provisional; Region: PRK11083 1427342001440 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342001441 active site 1427342001442 phosphorylation site [posttranslational modification] 1427342001443 intermolecular recognition site; other site 1427342001444 dimerization interface [polypeptide binding]; other site 1427342001445 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342001446 DNA binding site [nucleotide binding] 1427342001447 sensory histidine kinase CreC; Provisional; Region: PRK11100 1427342001448 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342001449 dimer interface [polypeptide binding]; other site 1427342001450 phosphorylation site [posttranslational modification] 1427342001451 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342001452 ATP binding site [chemical binding]; other site 1427342001453 G-X-G motif; other site 1427342001454 Inner membrane protein involved in colicin E2 resistance [Defense mechanisms]; Region: CreD; COG4452 1427342001455 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342001456 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 1427342001457 putative C-terminal domain interface [polypeptide binding]; other site 1427342001458 putative GSH binding site (G-site) [chemical binding]; other site 1427342001459 putative dimer interface [polypeptide binding]; other site 1427342001460 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 1427342001461 N-terminal domain interface [polypeptide binding]; other site 1427342001462 dimer interface [polypeptide binding]; other site 1427342001463 Streptogramin lyase [Defense mechanisms]; Region: Vgb; COG4257 1427342001464 Protein phosphatase 2C; Region: PP2C_2; pfam13672 1427342001465 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342001466 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 1427342001467 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342001468 N-terminal plug; other site 1427342001469 ligand-binding site [chemical binding]; other site 1427342001470 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342001471 FecR protein; Region: FecR; pfam04773 1427342001472 RNA polymerase sigma factor; Reviewed; Region: PRK12523 1427342001473 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342001474 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342001475 DNA binding residues [nucleotide binding] 1427342001476 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342001477 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1427342001478 C-terminal domain interface [polypeptide binding]; other site 1427342001479 GSH binding site (G-site) [chemical binding]; other site 1427342001480 dimer interface [polypeptide binding]; other site 1427342001481 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1427342001482 N-terminal domain interface [polypeptide binding]; other site 1427342001483 dimer interface [polypeptide binding]; other site 1427342001484 substrate binding pocket (H-site) [chemical binding]; other site 1427342001485 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342001486 CoenzymeA binding site [chemical binding]; other site 1427342001487 subunit interaction site [polypeptide binding]; other site 1427342001488 PHB binding site; other site 1427342001489 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342001490 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342001491 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily; solute-binding domain; Region: SLC-NCS1sbd_u1; cd11555 1427342001492 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342001493 Na binding site [ion binding]; other site 1427342001494 putative substrate binding site [chemical binding]; other site 1427342001495 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342001496 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; Region: PBP2_Pa0477; cd08468 1427342001497 putative substrate binding pocket [chemical binding]; other site 1427342001498 dimerization interface [polypeptide binding]; other site 1427342001499 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342001500 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342001501 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342001502 dimerization interface [polypeptide binding]; other site 1427342001503 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342001504 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 1427342001505 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 1427342001506 active site 1427342001507 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342001508 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342001509 Coenzyme A binding pocket [chemical binding]; other site 1427342001510 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 1427342001511 ACT domain; Region: ACT_6; pfam13740 1427342001512 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 1427342001513 Predicted permeases [General function prediction only]; Region: RarD; COG2962 1427342001514 EamA-like transporter family; Region: EamA; pfam00892 1427342001515 serine/threonine protein kinase; Provisional; Region: PRK11768 1427342001516 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 1427342001517 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 1427342001518 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 1427342001519 TOBE domain; Region: TOBE; cl01440 1427342001520 TOBE domain; Region: TOBE; cl01440 1427342001521 lipoprotein; Provisional; Region: PRK10759 1427342001522 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1427342001523 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342001524 active site 1427342001525 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342001526 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342001527 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 1427342001528 putative substrate binding pocket [chemical binding]; other site 1427342001529 dimerization interface [polypeptide binding]; other site 1427342001530 uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; Region: LamB_YcsF_like_2; cd11664 1427342001531 putative active site [active] 1427342001532 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342001533 carboxyltransferase (CT) interaction site; other site 1427342001534 biotinylation site [posttranslational modification]; other site 1427342001535 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional; Region: PRK12833 1427342001536 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342001537 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342001538 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1427342001539 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 1427342001540 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1427342001541 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 1427342001542 Fimbrial protein; Region: Fimbrial; pfam00419 1427342001543 Fimbrial protein; Region: Fimbrial; pfam00419 1427342001544 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1427342001545 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342001546 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 1427342001547 biotin synthase; Provisional; Region: PRK15108 1427342001548 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342001549 FeS/SAM binding site; other site 1427342001550 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 1427342001551 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1427342001552 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 1427342001553 substrate-cofactor binding pocket; other site 1427342001554 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001555 catalytic residue [active] 1427342001556 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342001557 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1427342001558 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001559 S-adenosylmethionine binding site [chemical binding]; other site 1427342001560 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 1427342001561 AAA domain; Region: AAA_26; pfam13500 1427342001562 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342001563 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342001564 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342001565 active site 1427342001566 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342001567 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342001568 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342001569 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342001570 active site 1427342001571 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342001572 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342001573 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342001574 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342001575 active site 1427342001576 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342001577 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342001578 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342001579 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 1427342001580 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 1427342001581 structural tetrad; other site 1427342001582 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 1427342001583 active site 1427342001584 SAM binding site [chemical binding]; other site 1427342001585 homodimer interface [polypeptide binding]; other site 1427342001586 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 1427342001587 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342001588 FeS/SAM binding site; other site 1427342001589 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342001590 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342001591 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342001592 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342001593 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 1427342001594 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342001595 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342001596 Cytochrome c551/c552 [Energy production and conversion]; Region: COG4654 1427342001597 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342001598 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342001599 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 1427342001600 MoxR-like ATPases [General function prediction only]; Region: COG0714 1427342001601 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342001602 Walker A motif; other site 1427342001603 ATP binding site [chemical binding]; other site 1427342001604 Walker B motif; other site 1427342001605 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 1427342001606 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 1427342001607 Subunit I/III interface [polypeptide binding]; other site 1427342001608 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342001609 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 1427342001610 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1427342001611 Low-spin heme binding site [chemical binding]; other site 1427342001612 D-pathway; other site 1427342001613 Putative water exit pathway; other site 1427342001614 Binuclear center (active site) [active] 1427342001615 K-pathway; other site 1427342001616 Putative proton exit pathway; other site 1427342001617 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 1427342001618 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 1427342001619 metal ion-dependent adhesion site (MIDAS); other site 1427342001620 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1427342001621 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342001622 ligand binding site [chemical binding]; other site 1427342001623 flexible hinge region; other site 1427342001624 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 1427342001625 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342001626 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342001627 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342001628 dimerization interface [polypeptide binding]; other site 1427342001629 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 1427342001630 MOSC domain; Region: MOSC; pfam03473 1427342001631 3-alpha domain; Region: 3-alpha; pfam03475 1427342001632 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 1427342001633 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342001634 inhibitor-cofactor binding pocket; inhibition site 1427342001635 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342001636 catalytic residue [active] 1427342001637 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 1427342001638 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 1427342001639 catalytic triad [active] 1427342001640 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342001641 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001642 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342001643 putative active site [active] 1427342001644 heme pocket [chemical binding]; other site 1427342001645 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001646 putative active site [active] 1427342001647 heme pocket [chemical binding]; other site 1427342001648 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342001649 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342001650 DNA binding residues [nucleotide binding] 1427342001651 dimerization interface [polypeptide binding]; other site 1427342001652 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342001653 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342001654 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342001655 non-specific DNA binding site [nucleotide binding]; other site 1427342001656 salt bridge; other site 1427342001657 sequence-specific DNA binding site [nucleotide binding]; other site 1427342001658 Cupin domain; Region: Cupin_2; pfam07883 1427342001659 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 1427342001660 Repair protein; Region: Repair_PSII; pfam04536 1427342001661 LemA family; Region: LemA; pfam04011 1427342001662 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 1427342001663 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 1427342001664 EamA-like transporter family; Region: EamA; pfam00892 1427342001665 Predicted membrane protein [Function unknown]; Region: COG3686 1427342001666 Cytochrome c556 [Energy production and conversion]; Region: COG3909 1427342001667 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 1427342001668 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 1427342001669 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1427342001670 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1427342001671 active site 1427342001672 metal binding site [ion binding]; metal-binding site 1427342001673 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 1427342001674 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 1427342001675 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 1427342001676 FAD binding pocket [chemical binding]; other site 1427342001677 FAD binding motif [chemical binding]; other site 1427342001678 phosphate binding motif [ion binding]; other site 1427342001679 beta-alpha-beta structure motif; other site 1427342001680 NAD binding pocket [chemical binding]; other site 1427342001681 S-adenosylmethionine synthetase; Validated; Region: PRK05250 1427342001682 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1427342001683 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1427342001684 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1427342001685 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342001686 putative DNA binding site [nucleotide binding]; other site 1427342001687 dimerization interface [polypeptide binding]; other site 1427342001688 putative Zn2+ binding site [ion binding]; other site 1427342001689 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1427342001690 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001691 S-adenosylmethionine binding site [chemical binding]; other site 1427342001692 transketolase; Reviewed; Region: PRK12753 1427342001693 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 1427342001694 TPP-binding site [chemical binding]; other site 1427342001695 dimer interface [polypeptide binding]; other site 1427342001696 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 1427342001697 PYR/PP interface [polypeptide binding]; other site 1427342001698 dimer interface [polypeptide binding]; other site 1427342001699 TPP binding site [chemical binding]; other site 1427342001700 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1427342001701 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 1427342001702 erythrose-4-phosphate dehydrogenase; Region: E4PD_g-proteo; TIGR01532 1427342001703 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 1427342001704 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1427342001705 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 1427342001706 Phosphoglycerate kinase; Region: PGK; pfam00162 1427342001707 substrate binding site [chemical binding]; other site 1427342001708 hinge regions; other site 1427342001709 ADP binding site [chemical binding]; other site 1427342001710 catalytic site [active] 1427342001711 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 1427342001712 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 1427342001713 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 1427342001714 intersubunit interface [polypeptide binding]; other site 1427342001715 active site 1427342001716 zinc binding site [ion binding]; other site 1427342001717 Na+ binding site [ion binding]; other site 1427342001718 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 1427342001719 SnoaL-like domain; Region: SnoaL_3; pfam13474 1427342001720 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342001721 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342001722 S-adenosylmethionine binding site [chemical binding]; other site 1427342001723 Predicted flavoproteins [General function prediction only]; Region: COG2081 1427342001724 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 1427342001725 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342001726 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 1427342001727 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 1427342001728 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342001729 motif II; other site 1427342001730 Protein of unknown function (DUF805); Region: DUF805; pfam05656 1427342001731 Cupin; Region: Cupin_6; pfam12852 1427342001732 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342001733 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342001734 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 1427342001735 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 1427342001736 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 1427342001737 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 1427342001738 Peptidase M60-like family; Region: M60-like; pfam13402 1427342001739 Nuclease-related domain; Region: NERD; pfam08378 1427342001740 Fic family protein [Function unknown]; Region: COG3177 1427342001741 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 1427342001742 Fic/DOC family; Region: Fic; pfam02661 1427342001743 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342001744 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342001745 substrate binding pocket [chemical binding]; other site 1427342001746 membrane-bound complex binding site; other site 1427342001747 hinge residues; other site 1427342001748 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001749 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342001750 putative active site [active] 1427342001751 heme pocket [chemical binding]; other site 1427342001752 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001753 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 1427342001754 putative active site [active] 1427342001755 heme pocket [chemical binding]; other site 1427342001756 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001757 putative active site [active] 1427342001758 heme pocket [chemical binding]; other site 1427342001759 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001760 putative active site [active] 1427342001761 heme pocket [chemical binding]; other site 1427342001762 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342001763 metal binding site [ion binding]; metal-binding site 1427342001764 active site 1427342001765 I-site; other site 1427342001766 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342001767 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1427342001768 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1427342001769 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1427342001770 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 1427342001771 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342001772 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1427342001773 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342001774 DNA binding residues [nucleotide binding] 1427342001775 DNA primase, catalytic core; Region: dnaG; TIGR01391 1427342001776 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1427342001777 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1427342001778 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 1427342001779 active site 1427342001780 metal binding site [ion binding]; metal-binding site 1427342001781 interdomain interaction site; other site 1427342001782 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 1427342001783 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 1427342001784 Yqey-like protein; Region: YqeY; pfam09424 1427342001785 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 1427342001786 UGMP family protein; Validated; Region: PRK09604 1427342001787 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1427342001788 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 1427342001789 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 1427342001790 homooctamer interface [polypeptide binding]; other site 1427342001791 active site 1427342001792 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 1427342001793 catalytic center binding site [active] 1427342001794 ATP binding site [chemical binding]; other site 1427342001795 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 1427342001796 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1427342001797 active site 1427342001798 NTP binding site [chemical binding]; other site 1427342001799 metal binding triad [ion binding]; metal-binding site 1427342001800 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1427342001801 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342001802 Zn2+ binding site [ion binding]; other site 1427342001803 Mg2+ binding site [ion binding]; other site 1427342001804 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 1427342001805 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 1427342001806 SpoVR family protein; Provisional; Region: PRK11767 1427342001807 hypothetical protein; Provisional; Region: PRK05325 1427342001808 PrkA family serine protein kinase; Provisional; Region: PRK15455 1427342001809 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 1427342001810 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 1427342001811 active site residue [active] 1427342001812 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 1427342001813 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 1427342001814 active site 1427342001815 metal binding site [ion binding]; metal-binding site 1427342001816 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 1427342001817 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1427342001818 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 1427342001819 S-adenosylmethionine binding site [chemical binding]; other site 1427342001820 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 1427342001821 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 1427342001822 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 1427342001823 SurA N-terminal domain; Region: SurA_N; pfam09312 1427342001824 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1427342001825 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1427342001826 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1427342001827 OstA-like protein; Region: OstA; cl00844 1427342001828 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1427342001829 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 1427342001830 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342001831 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 1427342001832 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 1427342001833 Substrate binding site; other site 1427342001834 metal-binding site 1427342001835 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 1427342001836 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 1427342001837 putative metal binding site [ion binding]; other site 1427342001838 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 1427342001839 HSP70 interaction site [polypeptide binding]; other site 1427342001840 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 1427342001841 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342001842 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342001843 substrate binding pocket [chemical binding]; other site 1427342001844 membrane-bound complex binding site; other site 1427342001845 hinge residues; other site 1427342001846 PAS domain S-box; Region: sensory_box; TIGR00229 1427342001847 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001848 putative active site [active] 1427342001849 heme pocket [chemical binding]; other site 1427342001850 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342001851 PAS fold; Region: PAS_3; pfam08447 1427342001852 putative active site [active] 1427342001853 heme pocket [chemical binding]; other site 1427342001854 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 1427342001855 Histidine kinase; Region: HisKA_3; pfam07730 1427342001856 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342001857 ATP binding site [chemical binding]; other site 1427342001858 Mg2+ binding site [ion binding]; other site 1427342001859 G-X-G motif; other site 1427342001860 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342001861 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342001862 active site 1427342001863 phosphorylation site [posttranslational modification] 1427342001864 intermolecular recognition site; other site 1427342001865 dimerization interface [polypeptide binding]; other site 1427342001866 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342001867 DNA binding residues [nucleotide binding] 1427342001868 dimerization interface [polypeptide binding]; other site 1427342001869 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342001870 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342001871 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1427342001872 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 1427342001873 Walker A/P-loop; other site 1427342001874 ATP binding site [chemical binding]; other site 1427342001875 Q-loop/lid; other site 1427342001876 ABC transporter signature motif; other site 1427342001877 Walker B; other site 1427342001878 D-loop; other site 1427342001879 H-loop/switch region; other site 1427342001880 Poxvirus L5 protein family; Region: Pox_L5; cl17406 1427342001881 TOBE domain; Region: TOBE_2; pfam08402 1427342001882 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342001883 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342001884 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342001885 dimer interface [polypeptide binding]; other site 1427342001886 conserved gate region; other site 1427342001887 putative PBP binding loops; other site 1427342001888 ABC-ATPase subunit interface; other site 1427342001889 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342001890 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342001891 dimer interface [polypeptide binding]; other site 1427342001892 conserved gate region; other site 1427342001893 putative PBP binding loops; other site 1427342001894 ABC-ATPase subunit interface; other site 1427342001895 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 1427342001896 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 1427342001897 substrate binding site [chemical binding]; other site 1427342001898 hexamer interface [polypeptide binding]; other site 1427342001899 metal binding site [ion binding]; metal-binding site 1427342001900 phosphoglycolate phosphatase; Provisional; Region: PRK13223 1427342001901 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342001902 motif II; other site 1427342001903 anthranilate synthase component I; Provisional; Region: PRK13565 1427342001904 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 1427342001905 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1427342001906 Pyocin activator protein PrtN; Region: PyocinActivator; pfam11112 1427342001907 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342001908 non-specific DNA binding site [nucleotide binding]; other site 1427342001909 Predicted transcriptional regulator [Transcription]; Region: COG2932 1427342001910 salt bridge; other site 1427342001911 sequence-specific DNA binding site [nucleotide binding]; other site 1427342001912 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1427342001913 Catalytic site [active] 1427342001914 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1427342001915 Predicted chitinase [General function prediction only]; Region: COG3179 1427342001916 catalytic residue [active] 1427342001917 Phage-related minor tail protein [Function unknown]; Region: COG5281 1427342001918 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 1427342001919 Phage-related minor tail protein [Function unknown]; Region: COG5281 1427342001920 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 1427342001921 Phage-related protein [Function unknown]; Region: COG4718 1427342001922 Phage-related protein [Function unknown]; Region: gp18; COG4672 1427342001923 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; Region: MPN_NLPC_P60; cd08073 1427342001924 MPN+ (JAMM) motif; other site 1427342001925 Zinc-binding site [ion binding]; other site 1427342001926 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1427342001927 NlpC/P60 family; Region: NLPC_P60; pfam00877 1427342001928 Phage-related protein, tail component [Function unknown]; Region: COG4723 1427342001929 Phage-related protein, tail component [Function unknown]; Region: COG4733 1427342001930 Putative phage tail protein; Region: Phage-tail_3; pfam13550 1427342001931 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 1427342001932 Interdomain contacts; other site 1427342001933 Cytokine receptor motif; other site 1427342001934 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 1427342001935 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 1427342001936 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1427342001937 glutamine binding [chemical binding]; other site 1427342001938 catalytic triad [active] 1427342001939 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 1427342001940 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1427342001941 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 1427342001942 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 1427342001943 active site 1427342001944 ribulose/triose binding site [chemical binding]; other site 1427342001945 phosphate binding site [ion binding]; other site 1427342001946 substrate (anthranilate) binding pocket [chemical binding]; other site 1427342001947 product (indole) binding pocket [chemical binding]; other site 1427342001948 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 1427342001949 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342001950 ligand binding site [chemical binding]; other site 1427342001951 flexible hinge region; other site 1427342001952 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 1427342001953 putative switch regulator; other site 1427342001954 non-specific DNA interactions [nucleotide binding]; other site 1427342001955 DNA binding site [nucleotide binding] 1427342001956 sequence specific DNA binding site [nucleotide binding]; other site 1427342001957 putative cAMP binding site [chemical binding]; other site 1427342001958 OsmC-like protein; Region: OsmC; cl00767 1427342001959 S-adenosylmethionine decarboxylase; Provisional; Region: PRK05462 1427342001960 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1427342001961 diiron binding motif [ion binding]; other site 1427342001962 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 1427342001963 nucleotide binding site/active site [active] 1427342001964 HIT family signature motif; other site 1427342001965 catalytic residue [active] 1427342001966 Ycf46; Provisional; Region: ycf46; CHL00195 1427342001967 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342001968 Walker A motif; other site 1427342001969 ATP binding site [chemical binding]; other site 1427342001970 Walker B motif; other site 1427342001971 arginine finger; other site 1427342001972 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 1427342001973 classical (c) SDRs; Region: SDR_c; cd05233 1427342001974 NAD(P) binding site [chemical binding]; other site 1427342001975 active site 1427342001976 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 1427342001977 Predicted membrane protein [Function unknown]; Region: COG3152 1427342001978 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 1427342001979 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 1427342001980 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 1427342001981 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 1427342001982 FMN binding site [chemical binding]; other site 1427342001983 substrate binding site [chemical binding]; other site 1427342001984 putative catalytic residue [active] 1427342001985 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 1427342001986 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 1427342001987 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1427342001988 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 1427342001989 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 1427342001990 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 1427342001991 Uncharacterized protein family (UPF0075); Region: UPF0075; pfam03702 1427342001992 putative peptidase; Provisional; Region: PRK11649 1427342001993 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 1427342001994 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342001995 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1427342001996 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1427342001997 active site 1427342001998 HIGH motif; other site 1427342001999 dimer interface [polypeptide binding]; other site 1427342002000 KMSKS motif; other site 1427342002001 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1427342002002 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1427342002003 pantothenate kinase; Reviewed; Region: PRK13322 1427342002004 Sporulation related domain; Region: SPOR; pfam05036 1427342002005 Sporulation related domain; Region: SPOR; pfam05036 1427342002006 Sporulation related domain; Region: SPOR; cl10051 1427342002007 elongation factor Tu; Reviewed; Region: PRK00049 1427342002008 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1427342002009 G1 box; other site 1427342002010 GEF interaction site [polypeptide binding]; other site 1427342002011 GTP/Mg2+ binding site [chemical binding]; other site 1427342002012 Switch I region; other site 1427342002013 G2 box; other site 1427342002014 G3 box; other site 1427342002015 Switch II region; other site 1427342002016 G4 box; other site 1427342002017 G5 box; other site 1427342002018 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 1427342002019 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 1427342002020 Antibiotic Binding Site [chemical binding]; other site 1427342002021 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 1427342002022 transcription termination/antitermination factor NusG; Region: nusG; TIGR00922 1427342002023 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1427342002024 putative homodimer interface [polypeptide binding]; other site 1427342002025 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1427342002026 heterodimer interface [polypeptide binding]; other site 1427342002027 homodimer interface [polypeptide binding]; other site 1427342002028 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1427342002029 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 1427342002030 23S rRNA interface [nucleotide binding]; other site 1427342002031 L7/L12 interface [polypeptide binding]; other site 1427342002032 putative thiostrepton binding site; other site 1427342002033 L25 interface [polypeptide binding]; other site 1427342002034 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 1427342002035 mRNA/rRNA interface [nucleotide binding]; other site 1427342002036 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 1427342002037 23S rRNA interface [nucleotide binding]; other site 1427342002038 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1427342002039 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 1427342002040 core dimer interface [polypeptide binding]; other site 1427342002041 peripheral dimer interface [polypeptide binding]; other site 1427342002042 L10 interface [polypeptide binding]; other site 1427342002043 L11 interface [polypeptide binding]; other site 1427342002044 putative EF-Tu interaction site [polypeptide binding]; other site 1427342002045 putative EF-G interaction site [polypeptide binding]; other site 1427342002046 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1427342002047 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 1427342002048 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1427342002049 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 1427342002050 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1427342002051 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 1427342002052 RPB3 interaction site [polypeptide binding]; other site 1427342002053 RPB1 interaction site [polypeptide binding]; other site 1427342002054 RPB11 interaction site [polypeptide binding]; other site 1427342002055 RPB10 interaction site [polypeptide binding]; other site 1427342002056 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1427342002057 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1427342002058 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1427342002059 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1427342002060 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1427342002061 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1427342002062 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1427342002063 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1427342002064 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1427342002065 DNA binding site [nucleotide binding] 1427342002066 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1427342002067 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 1427342002068 S17 interaction site [polypeptide binding]; other site 1427342002069 S8 interaction site; other site 1427342002070 16S rRNA interaction site [nucleotide binding]; other site 1427342002071 streptomycin interaction site [chemical binding]; other site 1427342002072 23S rRNA interaction site [nucleotide binding]; other site 1427342002073 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1427342002074 30S ribosomal protein S7; Validated; Region: PRK05302 1427342002075 elongation factor G; Reviewed; Region: PRK00007 1427342002076 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1427342002077 G1 box; other site 1427342002078 putative GEF interaction site [polypeptide binding]; other site 1427342002079 GTP/Mg2+ binding site [chemical binding]; other site 1427342002080 Switch I region; other site 1427342002081 G2 box; other site 1427342002082 G3 box; other site 1427342002083 Switch II region; other site 1427342002084 G4 box; other site 1427342002085 G5 box; other site 1427342002086 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 1427342002087 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 1427342002088 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 1427342002089 elongation factor Tu; Reviewed; Region: PRK00049 1427342002090 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1427342002091 G1 box; other site 1427342002092 GEF interaction site [polypeptide binding]; other site 1427342002093 GTP/Mg2+ binding site [chemical binding]; other site 1427342002094 Switch I region; other site 1427342002095 G2 box; other site 1427342002096 G3 box; other site 1427342002097 Switch II region; other site 1427342002098 G4 box; other site 1427342002099 G5 box; other site 1427342002100 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 1427342002101 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 1427342002102 Antibiotic Binding Site [chemical binding]; other site 1427342002103 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1427342002104 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1427342002105 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1427342002106 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1427342002107 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1427342002108 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1427342002109 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1427342002110 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1427342002111 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 1427342002112 putative translocon binding site; other site 1427342002113 protein-rRNA interface [nucleotide binding]; other site 1427342002114 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1427342002115 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 1427342002116 G-X-X-G motif; other site 1427342002117 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1427342002118 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 1427342002119 23S rRNA interface [nucleotide binding]; other site 1427342002120 5S rRNA interface [nucleotide binding]; other site 1427342002121 putative antibiotic binding site [chemical binding]; other site 1427342002122 L25 interface [polypeptide binding]; other site 1427342002123 L27 interface [polypeptide binding]; other site 1427342002124 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 1427342002125 23S rRNA interface [nucleotide binding]; other site 1427342002126 putative translocon interaction site; other site 1427342002127 signal recognition particle (SRP54) interaction site; other site 1427342002128 L23 interface [polypeptide binding]; other site 1427342002129 trigger factor interaction site; other site 1427342002130 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1427342002131 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1427342002132 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1427342002133 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1427342002134 RNA binding site [nucleotide binding]; other site 1427342002135 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1427342002136 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1427342002137 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1427342002138 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1427342002139 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1427342002140 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1427342002141 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1427342002142 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1427342002143 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 1427342002144 5S rRNA interface [nucleotide binding]; other site 1427342002145 23S rRNA interface [nucleotide binding]; other site 1427342002146 L5 interface [polypeptide binding]; other site 1427342002147 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1427342002148 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1427342002149 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1427342002150 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 1427342002151 23S rRNA binding site [nucleotide binding]; other site 1427342002152 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1427342002153 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1427342002154 SecY translocase; Region: SecY; pfam00344 1427342002155 Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]; Region: RpmJ; COG0257 1427342002156 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 1427342002157 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1427342002158 30S ribosomal protein S11; Validated; Region: PRK05309 1427342002159 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1427342002160 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1427342002161 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342002162 RNA binding surface [nucleotide binding]; other site 1427342002163 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1427342002164 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1427342002165 alphaNTD homodimer interface [polypeptide binding]; other site 1427342002166 alphaNTD - beta interaction site [polypeptide binding]; other site 1427342002167 alphaNTD - beta' interaction site [polypeptide binding]; other site 1427342002168 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1427342002169 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 1427342002170 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1427342002171 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 1427342002172 tetramer interface [polypeptide binding]; other site 1427342002173 heme binding pocket [chemical binding]; other site 1427342002174 NADPH binding site [chemical binding]; other site 1427342002175 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 1427342002176 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 1427342002177 heme binding site [chemical binding]; other site 1427342002178 ferroxidase pore; other site 1427342002179 ferroxidase diiron center [ion binding]; other site 1427342002180 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1427342002181 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1427342002182 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1427342002183 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1427342002184 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002185 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342002186 putative substrate translocation pore; other site 1427342002187 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1427342002188 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 1427342002189 ssDNA binding site [nucleotide binding]; other site 1427342002190 dimer interface [polypeptide binding]; other site 1427342002191 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1427342002192 salicylate biosynthesis isochorismate synthase; Validated; Region: PRK07054 1427342002193 isochorismate synthases; Region: isochor_syn; TIGR00543 1427342002194 isochorismate-pyruvate lyase; Reviewed; Region: PRK07075 1427342002195 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 1427342002196 Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntE; COG1021 1427342002197 2,3-dihydroxybenzoate-AMP ligase; Region: 23DHB-AMP_lg; cd05920 1427342002198 acyl-activating enzyme (AAE) consensus motif; other site 1427342002199 active site 1427342002200 AMP binding site [chemical binding]; other site 1427342002201 substrate binding site [chemical binding]; other site 1427342002202 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342002203 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342002204 Phosphopantetheine attachment site; Region: PP-binding; cl09936 1427342002205 Condensation domain; Region: Condensation; pfam00668 1427342002206 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342002207 Nonribosomal peptide synthase; Region: NRPS; pfam08415 1427342002208 The adenylation domain of nonribosomal peptide synthetases (NRPS), including Streptoalloteichus tallysomycin biosynthesis genes; Region: A_NRPS_TlmIV_like; cd12114 1427342002209 acyl-activating enzyme (AAE) consensus motif; other site 1427342002210 AMP binding site [chemical binding]; other site 1427342002211 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342002212 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342002213 Condensation domain; Region: Condensation; pfam00668 1427342002214 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342002215 Nonribosomal peptide synthase; Region: NRPS; pfam08415 1427342002216 The adenylation domain of nonribosomal peptide synthetases (NRPS), including Streptoalloteichus tallysomycin biosynthesis genes; Region: A_NRPS_TlmIV_like; cd12114 1427342002217 acyl-activating enzyme (AAE) consensus motif; other site 1427342002218 AMP binding site [chemical binding]; other site 1427342002219 Methyltransferase domain; Region: Methyltransf_12; pfam08242 1427342002220 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342002221 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342002222 thiazolinyl imide reductase; Region: thiaz-red; TIGR01761 1427342002223 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1427342002224 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1427342002225 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342002226 Walker A/P-loop; other site 1427342002227 ATP binding site [chemical binding]; other site 1427342002228 Q-loop/lid; other site 1427342002229 ABC transporter signature motif; other site 1427342002230 Walker B; other site 1427342002231 D-loop; other site 1427342002232 H-loop/switch region; other site 1427342002233 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1427342002234 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342002235 Walker A/P-loop; other site 1427342002236 ATP binding site [chemical binding]; other site 1427342002237 Q-loop/lid; other site 1427342002238 ABC transporter signature motif; other site 1427342002239 Walker B; other site 1427342002240 D-loop; other site 1427342002241 H-loop/switch region; other site 1427342002242 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 1427342002243 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342002244 N-terminal plug; other site 1427342002245 ligand-binding site [chemical binding]; other site 1427342002246 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342002247 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 1427342002248 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 1427342002249 hypothetical protein; Provisional; Region: PRK07538 1427342002250 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342002251 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 1427342002252 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 1427342002253 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 1427342002254 Phenazine biosynthesis-like protein; Region: PhzC-PhzF; pfam02567 1427342002255 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1427342002256 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1427342002257 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1427342002258 glutamine binding [chemical binding]; other site 1427342002259 catalytic triad [active] 1427342002260 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 1427342002261 hydrophobic substrate binding pocket; other site 1427342002262 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342002263 active site 1427342002264 conserved cis-peptide bond; other site 1427342002265 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 1427342002266 Phenazine biosynthesis protein A/B; Region: PHZA_PHZB; pfam03284 1427342002267 Phenazine biosynthesis protein A/B; Region: PHZA_PHZB; pfam03284 1427342002268 O-methyltransferase; Region: Methyltransf_2; pfam00891 1427342002269 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342002270 multidrug efflux protein; Reviewed; Region: PRK09579 1427342002271 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342002272 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342002273 Predicted membrane protein [Function unknown]; Region: COG2259 1427342002274 3-carboxymuconate cyclase [Carbohydrate transport and metabolism]; Region: COG2706 1427342002275 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342002276 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342002277 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 1427342002278 putative dimerization interface [polypeptide binding]; other site 1427342002279 Nitronate monooxygenase; Region: NMO; pfam03060 1427342002280 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 1427342002281 FMN binding site [chemical binding]; other site 1427342002282 substrate binding site [chemical binding]; other site 1427342002283 putative catalytic residue [active] 1427342002284 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1427342002285 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1427342002286 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342002287 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342002288 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342002289 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342002290 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342002291 active site 1427342002292 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342002293 acyl-CoA synthetase; Validated; Region: PRK08162 1427342002294 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 1427342002295 acyl-activating enzyme (AAE) consensus motif; other site 1427342002296 putative active site [active] 1427342002297 AMP binding site [chemical binding]; other site 1427342002298 putative CoA binding site [chemical binding]; other site 1427342002299 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342002300 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342002301 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342002302 putative active site [active] 1427342002303 heme pocket [chemical binding]; other site 1427342002304 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 1427342002305 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 1427342002306 putative active site [active] 1427342002307 heme pocket [chemical binding]; other site 1427342002308 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342002309 dimer interface [polypeptide binding]; other site 1427342002310 phosphorylation site [posttranslational modification] 1427342002311 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342002312 ATP binding site [chemical binding]; other site 1427342002313 Mg2+ binding site [ion binding]; other site 1427342002314 G-X-G motif; other site 1427342002315 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 1427342002316 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002317 active site 1427342002318 phosphorylation site [posttranslational modification] 1427342002319 intermolecular recognition site; other site 1427342002320 dimerization interface [polypeptide binding]; other site 1427342002321 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342002322 DNA binding residues [nucleotide binding] 1427342002323 dimerization interface [polypeptide binding]; other site 1427342002324 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342002325 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342002326 substrate binding pocket [chemical binding]; other site 1427342002327 membrane-bound complex binding site; other site 1427342002328 hinge residues; other site 1427342002329 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342002330 dimer interface [polypeptide binding]; other site 1427342002331 conserved gate region; other site 1427342002332 putative PBP binding loops; other site 1427342002333 ABC-ATPase subunit interface; other site 1427342002334 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342002335 dimer interface [polypeptide binding]; other site 1427342002336 conserved gate region; other site 1427342002337 putative PBP binding loops; other site 1427342002338 ABC-ATPase subunit interface; other site 1427342002339 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342002340 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342002341 Walker A/P-loop; other site 1427342002342 ATP binding site [chemical binding]; other site 1427342002343 Q-loop/lid; other site 1427342002344 ABC transporter signature motif; other site 1427342002345 Walker B; other site 1427342002346 D-loop; other site 1427342002347 H-loop/switch region; other site 1427342002348 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1427342002349 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 1427342002350 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342002351 putative monooxygenase; Reviewed; Region: PRK07045 1427342002352 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342002353 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 1427342002354 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342002355 NAD(P) binding site [chemical binding]; other site 1427342002356 catalytic residues [active] 1427342002357 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 1427342002358 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 1427342002359 inhibitor site; inhibition site 1427342002360 active site 1427342002361 dimer interface [polypeptide binding]; other site 1427342002362 catalytic residue [active] 1427342002363 benzoate transport; Region: 2A0115; TIGR00895 1427342002364 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002365 putative substrate translocation pore; other site 1427342002366 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342002367 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342002368 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 1427342002369 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342002370 DNA-binding site [nucleotide binding]; DNA binding site 1427342002371 FCD domain; Region: FCD; pfam07729 1427342002372 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 1427342002373 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 1427342002374 conserved cys residue [active] 1427342002375 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342002376 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342002377 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 1427342002378 active site 1427342002379 Transcriptional regulator [Transcription]; Region: PaiB; COG2808 1427342002380 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]; Region: COG3382 1427342002381 B3/4 domain; Region: B3_4; pfam03483 1427342002382 acetolactate synthase; Reviewed; Region: PRK08322 1427342002383 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342002384 PYR/PP interface [polypeptide binding]; other site 1427342002385 dimer interface [polypeptide binding]; other site 1427342002386 TPP binding site [chemical binding]; other site 1427342002387 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342002388 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 1427342002389 TPP-binding site [chemical binding]; other site 1427342002390 dimer interface [polypeptide binding]; other site 1427342002391 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342002392 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 1427342002393 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342002394 S-adenosylmethionine binding site [chemical binding]; other site 1427342002395 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1427342002396 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 1427342002397 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1427342002398 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342002399 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342002400 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 1427342002401 putative effector binding pocket; other site 1427342002402 putative dimerization interface [polypeptide binding]; other site 1427342002403 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 1427342002404 homotrimer interaction site [polypeptide binding]; other site 1427342002405 putative active site [active] 1427342002406 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1427342002407 putative catalytic site [active] 1427342002408 putative phosphate binding site [ion binding]; other site 1427342002409 active site 1427342002410 metal binding site A [ion binding]; metal-binding site 1427342002411 DNA binding site [nucleotide binding] 1427342002412 putative AP binding site [nucleotide binding]; other site 1427342002413 putative metal binding site B [ion binding]; other site 1427342002414 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 1427342002415 intracellular protease, PfpI family; Region: PfpI; TIGR01382 1427342002416 proposed catalytic triad [active] 1427342002417 conserved cys residue [active] 1427342002418 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1427342002419 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 1427342002420 Predicted transcriptional regulator [Transcription]; Region: COG1959 1427342002421 Transcriptional regulator; Region: Rrf2; pfam02082 1427342002422 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 1427342002423 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342002424 N-terminal plug; other site 1427342002425 ligand-binding site [chemical binding]; other site 1427342002426 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342002427 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342002428 active site 1427342002429 catalytic tetrad [active] 1427342002430 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342002431 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342002432 Coenzyme A binding pocket [chemical binding]; other site 1427342002433 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342002434 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342002435 DNA-binding site [nucleotide binding]; DNA binding site 1427342002436 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342002437 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342002438 homodimer interface [polypeptide binding]; other site 1427342002439 catalytic residue [active] 1427342002440 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 1427342002441 putative active site pocket [active] 1427342002442 dimerization interface [polypeptide binding]; other site 1427342002443 putative catalytic residue [active] 1427342002444 amidase; Validated; Region: PRK06565 1427342002445 Amidase; Region: Amidase; cl11426 1427342002446 short chain dehydrogenase; Provisional; Region: PRK07577 1427342002447 classical (c) SDRs; Region: SDR_c; cd05233 1427342002448 NAD(P) binding site [chemical binding]; other site 1427342002449 active site 1427342002450 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 1427342002451 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 1427342002452 ABC-ATPase subunit interface; other site 1427342002453 dimer interface [polypeptide binding]; other site 1427342002454 FecCD transport family; Region: FecCD; pfam01032 1427342002455 ABC-ATPase subunit interface; other site 1427342002456 dimer interface [polypeptide binding]; other site 1427342002457 putative PBP binding regions; other site 1427342002458 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 1427342002459 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 1427342002460 siderophore binding site; other site 1427342002461 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1427342002462 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1427342002463 Walker A/P-loop; other site 1427342002464 ATP binding site [chemical binding]; other site 1427342002465 Q-loop/lid; other site 1427342002466 ABC transporter signature motif; other site 1427342002467 Walker B; other site 1427342002468 D-loop; other site 1427342002469 H-loop/switch region; other site 1427342002470 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 1427342002471 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342002472 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342002473 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342002474 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 1427342002475 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 1427342002476 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 1427342002477 active site 1427342002478 non-prolyl cis peptide bond; other site 1427342002479 SH3 domain protein [Signal transduction mechanisms]; Region: COG3103 1427342002480 Bacterial SH3 domain; Region: SH3_3; pfam08239 1427342002481 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342002482 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 1427342002483 putative NAD(P) binding site [chemical binding]; other site 1427342002484 catalytic Zn binding site [ion binding]; other site 1427342002485 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 1427342002486 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342002487 E3 interaction surface; other site 1427342002488 lipoyl attachment site [posttranslational modification]; other site 1427342002489 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 1427342002490 nucleophilic elbow; other site 1427342002491 catalytic triad; other site 1427342002492 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 1427342002493 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 1427342002494 alpha subunit interface [polypeptide binding]; other site 1427342002495 TPP binding site [chemical binding]; other site 1427342002496 heterodimer interface [polypeptide binding]; other site 1427342002497 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1427342002498 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 1427342002499 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 1427342002500 tetramer interface [polypeptide binding]; other site 1427342002501 TPP-binding site [chemical binding]; other site 1427342002502 heterodimer interface [polypeptide binding]; other site 1427342002503 phosphorylation loop region [posttranslational modification] 1427342002504 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 1427342002505 ATP-NAD kinase; Region: NAD_kinase; pfam01513 1427342002506 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342002507 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342002508 NAD(P) binding site [chemical binding]; other site 1427342002509 active site 1427342002510 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 1427342002511 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342002512 Walker A motif; other site 1427342002513 ATP binding site [chemical binding]; other site 1427342002514 Walker B motif; other site 1427342002515 arginine finger; other site 1427342002516 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342002517 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342002518 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342002519 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342002520 putative effector binding pocket; other site 1427342002521 dimerization interface [polypeptide binding]; other site 1427342002522 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342002523 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 1427342002524 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39C; cd02419 1427342002525 putative active site [active] 1427342002526 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342002527 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1427342002528 Walker A/P-loop; other site 1427342002529 ATP binding site [chemical binding]; other site 1427342002530 Q-loop/lid; other site 1427342002531 ABC transporter signature motif; other site 1427342002532 Walker B; other site 1427342002533 D-loop; other site 1427342002534 H-loop/switch region; other site 1427342002535 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1427342002536 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342002537 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342002538 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1427342002539 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342002540 Cholesterol oxidase, substrate-binding; Region: Chol_subst-bind; pfam09129 1427342002541 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1427342002542 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1427342002543 active site 1427342002544 HIGH motif; other site 1427342002545 dimer interface [polypeptide binding]; other site 1427342002546 KMSKS motif; other site 1427342002547 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342002548 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 1427342002549 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002550 putative substrate translocation pore; other site 1427342002551 homoprotocatechuate degradation operon regulator, HpaR; Region: HpaR; TIGR02337 1427342002552 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342002553 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 1427342002554 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1427342002555 Low-spin heme binding site [chemical binding]; other site 1427342002556 Putative water exit pathway; other site 1427342002557 Binuclear center (active site) [active] 1427342002558 Putative proton exit pathway; other site 1427342002559 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342002560 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342002561 DNA-binding site [nucleotide binding]; DNA binding site 1427342002562 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342002563 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342002564 homodimer interface [polypeptide binding]; other site 1427342002565 catalytic residue [active] 1427342002566 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 1427342002567 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 1427342002568 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 1427342002569 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342002570 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342002571 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3749 1427342002572 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; Region: HpaI; TIGR02311 1427342002573 2-oxo-hepta-3-ene-1,7-dioic acid hydratase; Region: HpaH; TIGR02312 1427342002574 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 1427342002575 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002576 putative substrate translocation pore; other site 1427342002577 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 1427342002578 putative substrate binding pocket [chemical binding]; other site 1427342002579 trimer interface [polypeptide binding]; other site 1427342002580 The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate; Region: HPCD; cd07370 1427342002581 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 1427342002582 putative active site [active] 1427342002583 putative metal binding site [ion binding]; other site 1427342002584 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; Region: HpaE; TIGR02299 1427342002585 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 1427342002586 NAD binding site [chemical binding]; other site 1427342002587 catalytic residues [active] 1427342002588 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 1427342002589 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1427342002590 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 1427342002591 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 1427342002592 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 1427342002593 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342002594 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342002595 Aminoglycoside 3'-phosphotransferase (APH). The APH subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin...; Region: APH; cd05150 1427342002596 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342002597 active site 1427342002598 ATP binding site [chemical binding]; other site 1427342002599 antibiotic binding site [chemical binding]; other site 1427342002600 Predicted periplasmic protein [Function unknown]; Region: COG3904 1427342002601 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 1427342002602 GAF domain; Region: GAF; pfam01590 1427342002603 Phytochrome region; Region: PHY; pfam00360 1427342002604 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342002605 dimer interface [polypeptide binding]; other site 1427342002606 phosphorylation site [posttranslational modification] 1427342002607 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342002608 ATP binding site [chemical binding]; other site 1427342002609 Mg2+ binding site [ion binding]; other site 1427342002610 G-X-G motif; other site 1427342002611 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 1427342002612 heme binding pocket [chemical binding]; other site 1427342002613 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 1427342002614 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 1427342002615 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342002616 Coenzyme A binding pocket [chemical binding]; other site 1427342002617 putative arabinose transporter; Provisional; Region: PRK03545 1427342002618 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002619 putative substrate translocation pore; other site 1427342002620 CHASE domain; Region: CHASE; cl01369 1427342002621 PAS domain S-box; Region: sensory_box; TIGR00229 1427342002622 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342002623 putative active site [active] 1427342002624 heme pocket [chemical binding]; other site 1427342002625 PAS domain; Region: PAS_9; pfam13426 1427342002626 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342002627 putative active site [active] 1427342002628 heme pocket [chemical binding]; other site 1427342002629 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342002630 PAS fold; Region: PAS_3; pfam08447 1427342002631 putative active site [active] 1427342002632 heme pocket [chemical binding]; other site 1427342002633 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342002634 dimer interface [polypeptide binding]; other site 1427342002635 phosphorylation site [posttranslational modification] 1427342002636 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342002637 ATP binding site [chemical binding]; other site 1427342002638 Mg2+ binding site [ion binding]; other site 1427342002639 G-X-G motif; other site 1427342002640 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342002641 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002642 active site 1427342002643 phosphorylation site [posttranslational modification] 1427342002644 intermolecular recognition site; other site 1427342002645 dimerization interface [polypeptide binding]; other site 1427342002646 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342002647 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002648 active site 1427342002649 phosphorylation site [posttranslational modification] 1427342002650 intermolecular recognition site; other site 1427342002651 dimerization interface [polypeptide binding]; other site 1427342002652 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342002653 putative binding surface; other site 1427342002654 active site 1427342002655 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342002656 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 1427342002657 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342002658 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342002659 The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_beta_lactamase; cd08484 1427342002660 putative dimerization interface [polypeptide binding]; other site 1427342002661 putative substrate binding pocket [chemical binding]; other site 1427342002662 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 1427342002663 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 1427342002664 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342002665 Zn2+ binding site [ion binding]; other site 1427342002666 Mg2+ binding site [ion binding]; other site 1427342002667 SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate...; Region: SPARC_EC; cd00252 1427342002668 EF-hand Ca2+ binding loops [ion binding]; other site 1427342002669 FS-domain interface [polypeptide binding]; other site 1427342002670 Protein of unknown function (DUF692); Region: DUF692; pfam05114 1427342002671 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 1427342002672 DoxX; Region: DoxX; pfam07681 1427342002673 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 1427342002674 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342002675 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 1427342002676 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342002677 ATP binding site [chemical binding]; other site 1427342002678 Mg2+ binding site [ion binding]; other site 1427342002679 G-X-G motif; other site 1427342002680 osmolarity response regulator; Provisional; Region: ompR; PRK09468 1427342002681 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002682 active site 1427342002683 phosphorylation site [posttranslational modification] 1427342002684 intermolecular recognition site; other site 1427342002685 dimerization interface [polypeptide binding]; other site 1427342002686 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342002687 DNA binding site [nucleotide binding] 1427342002688 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342002689 choline dehydrogenase; Validated; Region: PRK02106 1427342002690 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342002691 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 1427342002692 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342002693 classical (c) SDRs; Region: SDR_c; cd05233 1427342002694 NAD(P) binding site [chemical binding]; other site 1427342002695 active site 1427342002696 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342002697 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 1427342002698 putative NAD(P) binding site [chemical binding]; other site 1427342002699 catalytic Zn binding site [ion binding]; other site 1427342002700 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342002701 D-galactonate transporter; Region: 2A0114; TIGR00893 1427342002702 putative substrate translocation pore; other site 1427342002703 Cupin domain; Region: Cupin_2; pfam07883 1427342002704 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342002705 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342002706 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342002707 CoenzymeA binding site [chemical binding]; other site 1427342002708 subunit interaction site [polypeptide binding]; other site 1427342002709 PHB binding site; other site 1427342002710 Flavin Reductases; Region: FlaRed; cl00801 1427342002711 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component; Region: HpaB-2; TIGR02310 1427342002712 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 1427342002713 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3553 1427342002714 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 1427342002715 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342002716 NAD(P) binding site [chemical binding]; other site 1427342002717 active site 1427342002718 aminotransferase; Validated; Region: PRK07046 1427342002719 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342002720 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342002721 catalytic residue [active] 1427342002722 Molybdenum cofactor biosynthesis protein F; Region: MoaF; pfam10703 1427342002723 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 1427342002724 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1427342002725 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342002726 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 1427342002727 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 1427342002728 PapC N-terminal domain; Region: PapC_N; pfam13954 1427342002729 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 1427342002730 PapC C-terminal domain; Region: PapC_C; pfam13953 1427342002731 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342002732 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 1427342002733 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 1427342002734 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342002735 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 1427342002736 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 1427342002737 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342002738 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002739 active site 1427342002740 phosphorylation site [posttranslational modification] 1427342002741 intermolecular recognition site; other site 1427342002742 dimerization interface [polypeptide binding]; other site 1427342002743 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342002744 DNA binding residues [nucleotide binding] 1427342002745 dimerization interface [polypeptide binding]; other site 1427342002746 short chain dehydrogenase; Provisional; Region: PRK08177 1427342002747 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 1427342002748 NAD(P) binding site [chemical binding]; other site 1427342002749 active site 1427342002750 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342002751 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 1427342002752 acyl-activating enzyme (AAE) consensus motif; other site 1427342002753 AMP binding site [chemical binding]; other site 1427342002754 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342002755 Putative dehydrogenase domain of multifunctional non-ribosomal peptide synthetases and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3320 1427342002756 Male sterility protein; Region: NAD_binding_4; pfam07993 1427342002757 NAD(P) binding site [chemical binding]; other site 1427342002758 active site 1427342002759 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342002760 non-specific DNA binding site [nucleotide binding]; other site 1427342002761 salt bridge; other site 1427342002762 sequence-specific DNA binding site [nucleotide binding]; other site 1427342002763 Methyltransferase domain; Region: Methyltransf_11; pfam08241 1427342002764 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342002765 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342002766 DNA binding residues [nucleotide binding] 1427342002767 dimerization interface [polypeptide binding]; other site 1427342002768 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1427342002769 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342002770 NAD(P) binding site [chemical binding]; other site 1427342002771 catalytic residues [active] 1427342002772 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342002773 Protein of unknown function (DUF3156); Region: DUF3156; pfam11354 1427342002774 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 1427342002775 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342002776 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 1427342002777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342002778 NAD(P) binding site [chemical binding]; other site 1427342002779 active site 1427342002780 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342002781 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1427342002782 NAD(P) binding site [chemical binding]; other site 1427342002783 active site 1427342002784 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 1427342002785 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1427342002786 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 1427342002787 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1427342002788 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1427342002789 FtsX-like permease family; Region: FtsX; pfam02687 1427342002790 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1427342002791 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342002792 Walker A/P-loop; other site 1427342002793 ATP binding site [chemical binding]; other site 1427342002794 Q-loop/lid; other site 1427342002795 ABC transporter signature motif; other site 1427342002796 Walker B; other site 1427342002797 D-loop; other site 1427342002798 H-loop/switch region; other site 1427342002799 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 1427342002800 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 1427342002801 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 1427342002802 Predicted methyltransferase [General function prediction only]; Region: COG3897 1427342002803 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 1427342002804 S-adenosylmethionine binding site [chemical binding]; other site 1427342002805 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 1427342002806 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 1427342002807 ATP cone domain; Region: ATP-cone; pfam03477 1427342002808 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 1427342002809 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 1427342002810 catalytic motif [active] 1427342002811 Zn binding site [ion binding]; other site 1427342002812 RibD C-terminal domain; Region: RibD_C; cl17279 1427342002813 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 1427342002814 Lumazine binding domain; Region: Lum_binding; pfam00677 1427342002815 Lumazine binding domain; Region: Lum_binding; pfam00677 1427342002816 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 1427342002817 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 1427342002818 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 1427342002819 dimerization interface [polypeptide binding]; other site 1427342002820 active site 1427342002821 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 1427342002822 homopentamer interface [polypeptide binding]; other site 1427342002823 active site 1427342002824 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1427342002825 thiamine monophosphate kinase; Provisional; Region: PRK05731 1427342002826 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 1427342002827 ATP binding site [chemical binding]; other site 1427342002828 dimerization interface [polypeptide binding]; other site 1427342002829 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1427342002830 tetramer interfaces [polypeptide binding]; other site 1427342002831 binuclear metal-binding site [ion binding]; other site 1427342002832 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342002833 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1427342002834 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1427342002835 catalytic motif [active] 1427342002836 Catalytic residue [active] 1427342002837 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 1427342002838 dimerization interface [polypeptide binding]; other site 1427342002839 active site 1427342002840 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 1427342002841 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 1427342002842 cobalamin binding residues [chemical binding]; other site 1427342002843 putative BtuC binding residues; other site 1427342002844 dimer interface [polypeptide binding]; other site 1427342002845 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 1427342002846 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 1427342002847 TPP-binding site; other site 1427342002848 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 1427342002849 PYR/PP interface [polypeptide binding]; other site 1427342002850 dimer interface [polypeptide binding]; other site 1427342002851 TPP binding site [chemical binding]; other site 1427342002852 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1427342002853 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1427342002854 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1427342002855 substrate binding pocket [chemical binding]; other site 1427342002856 chain length determination region; other site 1427342002857 substrate-Mg2+ binding site; other site 1427342002858 catalytic residues [active] 1427342002859 aspartate-rich region 1; other site 1427342002860 active site lid residues [active] 1427342002861 aspartate-rich region 2; other site 1427342002862 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1427342002863 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 1427342002864 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_1; cd03326 1427342002865 putative active site pocket [active] 1427342002866 metal binding site [ion binding]; metal-binding site 1427342002867 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 1427342002868 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 1427342002869 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 1427342002870 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1427342002871 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1427342002872 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1427342002873 Walker A/P-loop; other site 1427342002874 ATP binding site [chemical binding]; other site 1427342002875 Q-loop/lid; other site 1427342002876 ABC transporter signature motif; other site 1427342002877 Walker B; other site 1427342002878 D-loop; other site 1427342002879 H-loop/switch region; other site 1427342002880 CHASE2 domain; Region: CHASE2; pfam05226 1427342002881 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 1427342002882 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1427342002883 PAS domain; Region: PAS_8; pfam13188 1427342002884 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342002885 dimer interface [polypeptide binding]; other site 1427342002886 phosphorylation site [posttranslational modification] 1427342002887 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342002888 ATP binding site [chemical binding]; other site 1427342002889 Mg2+ binding site [ion binding]; other site 1427342002890 G-X-G motif; other site 1427342002891 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 1427342002892 FecR protein; Region: FecR; pfam04773 1427342002893 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 1427342002894 amphipathic channel; other site 1427342002895 Asn-Pro-Ala signature motifs; other site 1427342002896 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342002897 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342002898 active site 1427342002899 phosphorylation site [posttranslational modification] 1427342002900 intermolecular recognition site; other site 1427342002901 dimerization interface [polypeptide binding]; other site 1427342002902 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342002903 DNA binding site [nucleotide binding] 1427342002904 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 1427342002905 dimer interface [polypeptide binding]; other site 1427342002906 substrate binding site [chemical binding]; other site 1427342002907 metal binding sites [ion binding]; metal-binding site 1427342002908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3228 1427342002909 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1427342002910 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1427342002911 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342002912 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342002913 substrate binding pocket [chemical binding]; other site 1427342002914 membrane-bound complex binding site; other site 1427342002915 hinge residues; other site 1427342002916 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342002917 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342002918 Coenzyme A binding pocket [chemical binding]; other site 1427342002919 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 1427342002920 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 1427342002921 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 1427342002922 ethanolamine permease; Region: 2A0305; TIGR00908 1427342002923 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1427342002924 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1427342002925 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1427342002926 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342002927 NAD(P) binding site [chemical binding]; other site 1427342002928 catalytic residues [active] 1427342002929 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 1427342002930 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342002931 putative active site [active] 1427342002932 heme pocket [chemical binding]; other site 1427342002933 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342002934 Walker A motif; other site 1427342002935 ATP binding site [chemical binding]; other site 1427342002936 Walker B motif; other site 1427342002937 arginine finger; other site 1427342002938 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342002939 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342002940 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1427342002941 aromatic acid decarboxylase; Validated; Region: PRK05920 1427342002942 Flavoprotein; Region: Flavoprotein; pfam02441 1427342002943 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5645 1427342002944 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 1427342002945 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 1427342002946 NAD binding site [chemical binding]; other site 1427342002947 active site 1427342002948 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 1427342002949 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 1427342002950 MORN repeat; Region: MORN; cl14787 1427342002951 Peptidase C13 family; Region: Peptidase_C13; pfam01650 1427342002952 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 1427342002953 putative active site [active] 1427342002954 putative catalytic site [active] 1427342002955 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 1427342002956 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 1427342002957 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1427342002958 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1427342002959 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 1427342002960 active site 1427342002961 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1427342002962 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1427342002963 active site 1427342002964 DNA binding site [nucleotide binding] 1427342002965 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 1427342002966 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 1427342002967 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342002968 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 1427342002969 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 1427342002970 putative catalytic cysteine [active] 1427342002971 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 1427342002972 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 1427342002973 active site 1427342002974 (T/H)XGH motif; other site 1427342002975 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 1427342002976 Uncharacterized conserved protein [Function unknown]; Region: COG1576 1427342002977 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1427342002978 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1427342002979 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1427342002980 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1427342002981 Transglycosylase SLT domain; Region: SLT_2; pfam13406 1427342002982 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342002983 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342002984 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1427342002985 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1427342002986 Sporulation related domain; Region: SPOR; pfam05036 1427342002987 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 1427342002988 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1427342002989 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 1427342002990 hypothetical protein; Provisional; Region: PRK00341 1427342002991 lipoate-protein ligase B; Provisional; Region: PRK14342 1427342002992 lipoyl synthase; Provisional; Region: PRK05481 1427342002993 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342002994 FeS/SAM binding site; other site 1427342002995 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342002996 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342002997 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342002998 dimerization interface [polypeptide binding]; other site 1427342002999 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342003000 Transglycosylase SLT domain; Region: SLT_2; pfam13406 1427342003001 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342003002 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342003003 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1427342003004 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3036 1427342003005 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 1427342003006 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 1427342003007 Rare lipoprotein B [Cell envelope biogenesis, outer membrane]; Region: RlpB; COG2980 1427342003008 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1427342003009 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1427342003010 HIGH motif; other site 1427342003011 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1427342003012 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1427342003013 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1427342003014 active site 1427342003015 KMSKS motif; other site 1427342003016 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1427342003017 tRNA binding surface [nucleotide binding]; other site 1427342003018 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1427342003019 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 1427342003020 putative active site [active] 1427342003021 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1427342003022 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1427342003023 putative active site [active] 1427342003024 catalytic triad [active] 1427342003025 putative dimer interface [polypeptide binding]; other site 1427342003026 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 1427342003027 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 1427342003028 Transporter associated domain; Region: CorC_HlyC; smart01091 1427342003029 metal-binding heat shock protein; Provisional; Region: PRK00016 1427342003030 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 1427342003031 PhoH-like protein; Region: PhoH; pfam02562 1427342003032 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1427342003033 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1427342003034 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342003035 FeS/SAM binding site; other site 1427342003036 TRAM domain; Region: TRAM; pfam01938 1427342003037 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4517 1427342003038 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1427342003039 Sel1-like repeats; Region: SEL1; smart00671 1427342003040 Sel1-like repeats; Region: SEL1; smart00671 1427342003041 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1427342003042 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342003043 inhibitor-cofactor binding pocket; inhibition site 1427342003044 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342003045 catalytic residue [active] 1427342003046 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 1427342003047 thiamine phosphate binding site [chemical binding]; other site 1427342003048 active site 1427342003049 pyrophosphate binding site [ion binding]; other site 1427342003050 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 1427342003051 substrate binding site [chemical binding]; other site 1427342003052 dimer interface [polypeptide binding]; other site 1427342003053 ATP binding site [chemical binding]; other site 1427342003054 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 1427342003055 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 1427342003056 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342003057 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342003058 dimer interface [polypeptide binding]; other site 1427342003059 phosphorylation site [posttranslational modification] 1427342003060 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342003061 ATP binding site [chemical binding]; other site 1427342003062 Mg2+ binding site [ion binding]; other site 1427342003063 G-X-G motif; other site 1427342003064 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342003065 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342003066 active site 1427342003067 phosphorylation site [posttranslational modification] 1427342003068 intermolecular recognition site; other site 1427342003069 dimerization interface [polypeptide binding]; other site 1427342003070 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342003071 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342003072 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 1427342003073 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342003074 active site 1427342003075 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342003076 CoenzymeA binding site [chemical binding]; other site 1427342003077 subunit interaction site [polypeptide binding]; other site 1427342003078 PHB binding site; other site 1427342003079 AMP nucleosidase; Provisional; Region: PRK08292 1427342003080 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 1427342003081 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 1427342003082 SEC-C motif; Region: SEC-C; pfam02810 1427342003083 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1427342003084 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1427342003085 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1427342003086 pseudouridine synthase; Region: TIGR00093 1427342003087 active site 1427342003088 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 1427342003089 heme-binding site [chemical binding]; other site 1427342003090 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 1427342003091 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342003092 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342003093 putative DNA binding site [nucleotide binding]; other site 1427342003094 putative Zn2+ binding site [ion binding]; other site 1427342003095 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342003096 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1427342003097 Cation efflux family; Region: Cation_efflux; cl00316 1427342003098 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 1427342003099 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342003100 ATP binding site [chemical binding]; other site 1427342003101 putative Mg++ binding site [ion binding]; other site 1427342003102 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342003103 nucleotide binding region [chemical binding]; other site 1427342003104 ATP-binding site [chemical binding]; other site 1427342003105 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 1427342003106 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 1427342003107 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 1427342003108 active site 1427342003109 catalytic residues [active] 1427342003110 DNA binding site [nucleotide binding] 1427342003111 Int/Topo IB signature motif; other site 1427342003112 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 1427342003113 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 1427342003114 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1427342003115 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 1427342003116 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 1427342003117 Transposase domain (DUF772); Region: DUF772; pfam05598 1427342003118 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 1427342003119 Thermostable Phosphite Dehydrogenase; Region: PTDH; cd12157 1427342003120 homodimer interface [polypeptide binding]; other site 1427342003121 ligand binding site [chemical binding]; other site 1427342003122 NAD binding site [chemical binding]; other site 1427342003123 catalytic site [active] 1427342003124 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 1427342003125 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342003126 dimer interface [polypeptide binding]; other site 1427342003127 conserved gate region; other site 1427342003128 putative PBP binding loops; other site 1427342003129 ABC-ATPase subunit interface; other site 1427342003130 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 1427342003131 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 1427342003132 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 1427342003133 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 1427342003134 Walker A/P-loop; other site 1427342003135 ATP binding site [chemical binding]; other site 1427342003136 Q-loop/lid; other site 1427342003137 ABC transporter signature motif; other site 1427342003138 Walker B; other site 1427342003139 D-loop; other site 1427342003140 H-loop/switch region; other site 1427342003141 Transposase domain (DUF772); Region: DUF772; pfam05598 1427342003142 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 1427342003143 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 1427342003144 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 1427342003145 putative active site [active] 1427342003146 putative NTP binding site [chemical binding]; other site 1427342003147 putative nucleic acid binding site [nucleotide binding]; other site 1427342003148 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 1427342003149 cyclase homology domain; Region: CHD; cd07302 1427342003150 nucleotidyl binding site; other site 1427342003151 metal binding site [ion binding]; metal-binding site 1427342003152 dimer interface [polypeptide binding]; other site 1427342003153 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 1427342003154 cyclase homology domain; Region: CHD; cd07302 1427342003155 nucleotidyl binding site; other site 1427342003156 metal binding site [ion binding]; metal-binding site 1427342003157 dimer interface [polypeptide binding]; other site 1427342003158 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1427342003159 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342003160 ligand binding site [chemical binding]; other site 1427342003161 flexible hinge region; other site 1427342003162 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; cl17861 1427342003163 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342003164 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1427342003165 putative metal binding site [ion binding]; other site 1427342003166 short chain dehydrogenase; Provisional; Region: PRK06181 1427342003167 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342003168 NAD(P) binding site [chemical binding]; other site 1427342003169 active site 1427342003170 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 1427342003171 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342003172 dimethyl sulfone monooxygenase SfnG; Region: LLM_DMSO2_sfnG; TIGR04021 1427342003173 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342003174 active site 1427342003175 dimer interface [polypeptide binding]; other site 1427342003176 non-prolyl cis peptide bond; other site 1427342003177 insertion regions; other site 1427342003178 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342003179 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 1427342003180 catalytic triad [active] 1427342003181 conserved cis-peptide bond; other site 1427342003182 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3416 1427342003183 Uncharacterized conserved protein [Function unknown]; Region: COG1432 1427342003184 LabA_like proteins; Region: LabA_like/DUF88; cl10034 1427342003185 putative metal binding site [ion binding]; other site 1427342003186 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342003187 ATP binding site [chemical binding]; other site 1427342003188 Mg++ binding site [ion binding]; other site 1427342003189 motif III; other site 1427342003190 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342003191 nucleotide binding region [chemical binding]; other site 1427342003192 ATP-binding site [chemical binding]; other site 1427342003193 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 1427342003194 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342003195 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342003196 active site 1427342003197 phosphorylation site [posttranslational modification] 1427342003198 intermolecular recognition site; other site 1427342003199 dimerization interface [polypeptide binding]; other site 1427342003200 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342003201 DNA binding residues [nucleotide binding] 1427342003202 dimerization interface [polypeptide binding]; other site 1427342003203 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342003204 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342003205 active site 1427342003206 phosphorylation site [posttranslational modification] 1427342003207 intermolecular recognition site; other site 1427342003208 dimerization interface [polypeptide binding]; other site 1427342003209 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342003210 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 1427342003211 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003212 substrate binding pocket [chemical binding]; other site 1427342003213 membrane-bound complex binding site; other site 1427342003214 hinge residues; other site 1427342003215 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003216 substrate binding pocket [chemical binding]; other site 1427342003217 membrane-bound complex binding site; other site 1427342003218 hinge residues; other site 1427342003219 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342003220 putative active site [active] 1427342003221 heme pocket [chemical binding]; other site 1427342003222 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342003223 dimer interface [polypeptide binding]; other site 1427342003224 phosphorylation site [posttranslational modification] 1427342003225 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342003226 ATP binding site [chemical binding]; other site 1427342003227 Mg2+ binding site [ion binding]; other site 1427342003228 G-X-G motif; other site 1427342003229 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342003230 active site 1427342003231 phosphorylation site [posttranslational modification] 1427342003232 intermolecular recognition site; other site 1427342003233 dimerization interface [polypeptide binding]; other site 1427342003234 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342003235 putative binding surface; other site 1427342003236 active site 1427342003237 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 1427342003238 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 1427342003239 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342003240 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 1427342003241 NADPH bind site [chemical binding]; other site 1427342003242 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 1427342003243 putative FMN binding site [chemical binding]; other site 1427342003244 NADPH bind site [chemical binding]; other site 1427342003245 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 1427342003246 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 1427342003247 active site 1427342003248 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 1427342003249 catalytic triad [active] 1427342003250 dimer interface [polypeptide binding]; other site 1427342003251 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342003252 active site 1427342003253 motif I; other site 1427342003254 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 1427342003255 motif II; other site 1427342003256 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 1427342003257 IHF dimer interface [polypeptide binding]; other site 1427342003258 IHF - DNA interface [nucleotide binding]; other site 1427342003259 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342003260 active site 1427342003261 ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: TauA; COG4521 1427342003262 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003263 substrate binding pocket [chemical binding]; other site 1427342003264 membrane-bound complex binding site; other site 1427342003265 hinge residues; other site 1427342003266 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 1427342003267 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342003268 Walker A/P-loop; other site 1427342003269 ATP binding site [chemical binding]; other site 1427342003270 Q-loop/lid; other site 1427342003271 ABC transporter signature motif; other site 1427342003272 Walker B; other site 1427342003273 D-loop; other site 1427342003274 H-loop/switch region; other site 1427342003275 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342003276 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342003277 dimer interface [polypeptide binding]; other site 1427342003278 conserved gate region; other site 1427342003279 putative PBP binding loops; other site 1427342003280 ABC-ATPase subunit interface; other site 1427342003281 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342003282 taurine dioxygenase; Reviewed; Region: tauD; PRK09553 1427342003283 Predicted membrane protein [Function unknown]; Region: COG1297 1427342003284 BCCT family transporter; Region: BCCT; cl00569 1427342003285 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 1427342003286 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342003287 Walker A motif; other site 1427342003288 ATP binding site [chemical binding]; other site 1427342003289 Walker B motif; other site 1427342003290 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1427342003291 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1427342003292 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1427342003293 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1427342003294 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1427342003295 Protein of unknown function (DUF2474); Region: DUF2474; pfam10617 1427342003296 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342003297 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342003298 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342003299 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342003300 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342003301 putative substrate translocation pore; other site 1427342003302 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 1427342003303 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342003304 dimer interface [polypeptide binding]; other site 1427342003305 active site 1427342003306 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 1427342003307 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 1427342003308 dimer interface [polypeptide binding]; other site 1427342003309 acyl-activating enzyme (AAE) consensus motif; other site 1427342003310 putative active site [active] 1427342003311 AMP binding site [chemical binding]; other site 1427342003312 putative CoA binding site [chemical binding]; other site 1427342003313 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 1427342003314 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 1427342003315 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 1427342003316 AAA ATPase domain; Region: AAA_16; pfam13191 1427342003317 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342003318 DNA binding residues [nucleotide binding] 1427342003319 dimerization interface [polypeptide binding]; other site 1427342003320 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1427342003321 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342003322 metal-binding site [ion binding] 1427342003323 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1427342003324 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342003325 metal-binding site [ion binding] 1427342003326 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342003327 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1427342003328 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 1427342003329 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 1427342003330 putative active site [active] 1427342003331 PhoH-like protein; Region: PhoH; pfam02562 1427342003332 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 1427342003333 trimer interface [polypeptide binding]; other site 1427342003334 dimer interface [polypeptide binding]; other site 1427342003335 putative active site [active] 1427342003336 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 1427342003337 MoaE interaction surface [polypeptide binding]; other site 1427342003338 MoeB interaction surface [polypeptide binding]; other site 1427342003339 thiocarboxylated glycine; other site 1427342003340 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 1427342003341 MoaE homodimer interface [polypeptide binding]; other site 1427342003342 MoaD interaction [polypeptide binding]; other site 1427342003343 active site residues [active] 1427342003344 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 1427342003345 MPT binding site; other site 1427342003346 trimer interface [polypeptide binding]; other site 1427342003347 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 1427342003348 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 1427342003349 dimer interface [polypeptide binding]; other site 1427342003350 putative functional site; other site 1427342003351 putative MPT binding site; other site 1427342003352 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 1427342003353 Peptidase family U32; Region: Peptidase_U32; pfam01136 1427342003354 putative protease; Provisional; Region: PRK15447 1427342003355 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 1427342003356 Putative lipid carrier protein [Lipid metabolism]; Region: COG3154 1427342003357 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 1427342003358 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 1427342003359 putative active site [active] 1427342003360 putative metal binding site [ion binding]; other site 1427342003361 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1427342003362 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 1427342003363 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 1427342003364 generic binding surface I; other site 1427342003365 generic binding surface II; other site 1427342003366 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 1427342003367 putative active site [active] 1427342003368 putative catalytic site [active] 1427342003369 putative Mg binding site IVb [ion binding]; other site 1427342003370 putative phosphate binding site [ion binding]; other site 1427342003371 putative DNA binding site [nucleotide binding]; other site 1427342003372 putative Mg binding site IVa [ion binding]; other site 1427342003373 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 1427342003374 Uncharacterized conserved protein [Function unknown]; Region: COG4104 1427342003375 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 1427342003376 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 1427342003377 G1 box; other site 1427342003378 putative GEF interaction site [polypeptide binding]; other site 1427342003379 GTP/Mg2+ binding site [chemical binding]; other site 1427342003380 Switch I region; other site 1427342003381 G2 box; other site 1427342003382 G3 box; other site 1427342003383 Switch II region; other site 1427342003384 G4 box; other site 1427342003385 G5 box; other site 1427342003386 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 1427342003387 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; pfam08816 1427342003388 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1427342003389 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342003390 N-terminal plug; other site 1427342003391 ligand-binding site [chemical binding]; other site 1427342003392 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342003393 FecR protein; Region: FecR; pfam04773 1427342003394 RNA polymerase sigma factor; Provisional; Region: PRK12528 1427342003395 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342003396 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342003397 DNA binding residues [nucleotide binding] 1427342003398 DNA-binding transcriptional regulator SoxS; Provisional; Region: PRK10219 1427342003399 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342003400 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 1427342003401 EamA-like transporter family; Region: EamA; pfam00892 1427342003402 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 1427342003403 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 1427342003404 dimerization interface [polypeptide binding]; other site 1427342003405 ligand binding site [chemical binding]; other site 1427342003406 NADP binding site [chemical binding]; other site 1427342003407 catalytic site [active] 1427342003408 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342003409 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342003410 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342003411 putative effector binding pocket; other site 1427342003412 dimerization interface [polypeptide binding]; other site 1427342003413 Outer membrane efflux protein; Region: OEP; pfam02321 1427342003414 Outer membrane efflux protein; Region: OEP; pfam02321 1427342003415 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342003416 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342003417 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 1427342003418 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1427342003419 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342003420 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342003421 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 1427342003422 ATP-binding cassette domain of the osmoprotectant transporter; Region: ABC_OpuCA_Osmoprotection; cd03295 1427342003423 Walker A/P-loop; other site 1427342003424 ATP binding site [chemical binding]; other site 1427342003425 Q-loop/lid; other site 1427342003426 ABC transporter signature motif; other site 1427342003427 Walker B; other site 1427342003428 D-loop; other site 1427342003429 H-loop/switch region; other site 1427342003430 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc; cd04582 1427342003431 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342003432 dimer interface [polypeptide binding]; other site 1427342003433 conserved gate region; other site 1427342003434 ABC-ATPase subunit interface; other site 1427342003435 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 1427342003436 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342003437 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342003438 ABC-ATPase subunit interface; other site 1427342003439 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1427342003440 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1427342003441 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1427342003442 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1427342003443 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 1427342003444 Protein tyrosine/serine phosphatase [Signal transduction mechanisms]; Region: COG2365 1427342003445 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 1427342003446 active site 1427342003447 short chain dehydrogenase; Provisional; Region: PRK05693 1427342003448 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1427342003449 NADP binding site [chemical binding]; other site 1427342003450 active site 1427342003451 steroid binding site; other site 1427342003452 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342003453 Uncharacterized conserved protein [Function unknown]; Region: COG4273 1427342003454 transcriptional regulator NarL; Provisional; Region: PRK10651 1427342003455 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342003456 active site 1427342003457 phosphorylation site [posttranslational modification] 1427342003458 intermolecular recognition site; other site 1427342003459 dimerization interface [polypeptide binding]; other site 1427342003460 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342003461 DNA binding residues [nucleotide binding] 1427342003462 dimerization interface [polypeptide binding]; other site 1427342003463 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 1427342003464 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 1427342003465 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342003466 dimerization interface [polypeptide binding]; other site 1427342003467 Histidine kinase; Region: HisKA_3; pfam07730 1427342003468 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342003469 ATP binding site [chemical binding]; other site 1427342003470 Mg2+ binding site [ion binding]; other site 1427342003471 G-X-G motif; other site 1427342003472 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 1427342003473 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342003474 putative substrate translocation pore; other site 1427342003475 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 1427342003476 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 1427342003477 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 1427342003478 [4Fe-4S] binding site [ion binding]; other site 1427342003479 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342003480 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342003481 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342003482 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342003483 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 1427342003484 molybdopterin cofactor binding site; other site 1427342003485 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 1427342003486 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 1427342003487 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 1427342003488 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 1427342003489 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1427342003490 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 1427342003491 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342003492 FeS/SAM binding site; other site 1427342003493 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 1427342003494 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 1427342003495 Integrase core domain; Region: rve; pfam00665 1427342003496 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 1427342003497 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1427342003498 catalytic residues [active] 1427342003499 catalytic nucleophile [active] 1427342003500 Presynaptic Site I dimer interface [polypeptide binding]; other site 1427342003501 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 1427342003502 Synaptic Flat tetramer interface [polypeptide binding]; other site 1427342003503 Synaptic Site I dimer interface [polypeptide binding]; other site 1427342003504 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 1427342003505 DNA-binding interface [nucleotide binding]; DNA binding site 1427342003506 Colicin-like bacteriocin tRNase domain; Region: Cloacin; pfam03515 1427342003507 S-type Pyocin; Region: Pyocin_S; pfam06958 1427342003508 Colicin C terminal ribonuclease domain; Region: Colicin_C; pfam12106 1427342003509 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 1427342003510 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003511 substrate binding pocket [chemical binding]; other site 1427342003512 membrane-bound complex binding site; other site 1427342003513 hinge residues; other site 1427342003514 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 1427342003515 YheO-like PAS domain; Region: PAS_6; pfam08348 1427342003516 HTH domain; Region: HTH_22; pfam13309 1427342003517 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342003518 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342003519 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 1427342003520 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 1427342003521 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 1427342003522 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342003523 ATP binding site [chemical binding]; other site 1427342003524 Mg++ binding site [ion binding]; other site 1427342003525 motif III; other site 1427342003526 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342003527 nucleotide binding region [chemical binding]; other site 1427342003528 ATP-binding site [chemical binding]; other site 1427342003529 AMP-binding domain protein; Validated; Region: PRK07529 1427342003530 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342003531 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_4; cd05944 1427342003532 acyl-activating enzyme (AAE) consensus motif; other site 1427342003533 putative AMP binding site [chemical binding]; other site 1427342003534 putative active site [active] 1427342003535 putative CoA binding site [chemical binding]; other site 1427342003536 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 1427342003537 putative hydrolase; Provisional; Region: PRK11460 1427342003538 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1427342003539 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003540 substrate binding pocket [chemical binding]; other site 1427342003541 membrane-bound complex binding site; other site 1427342003542 hinge residues; other site 1427342003543 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1427342003544 SnoaL-like domain; Region: SnoaL_2; pfam12680 1427342003545 GST_N family, Metaxin subfamily, Metaxin-like proteins; a heterogenous group of proteins, predominantly uncharacterized, with similarity to metaxins and GSTs. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It...; Region: GST_N_Metaxin_like; cd03080 1427342003546 putative C-terminal domain interface [polypeptide binding]; other site 1427342003547 putative GSH binding site [chemical binding]; other site 1427342003548 putative dimer interface [polypeptide binding]; other site 1427342003549 C-terminal, alpha helical domain of Metaxin and related proteins; Region: GST_C_Metaxin; cd03193 1427342003550 putative N-terminal domain interface [polypeptide binding]; other site 1427342003551 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 1427342003552 putative active site [active] 1427342003553 GIY-YIG motif/motif A; other site 1427342003554 putative metal binding site [ion binding]; other site 1427342003555 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 1427342003556 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1427342003557 trimer interface [polypeptide binding]; other site 1427342003558 active site 1427342003559 substrate binding site [chemical binding]; other site 1427342003560 CoA binding site [chemical binding]; other site 1427342003561 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342003562 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1427342003563 C-terminal domain interface [polypeptide binding]; other site 1427342003564 GSH binding site (G-site) [chemical binding]; other site 1427342003565 dimer interface [polypeptide binding]; other site 1427342003566 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1427342003567 substrate binding pocket (H-site) [chemical binding]; other site 1427342003568 N-terminal domain interface [polypeptide binding]; other site 1427342003569 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_2; cd02433 1427342003570 Nucleoid-associated protein [General function prediction only]; Region: COG3081 1427342003571 nucleoid-associated protein NdpA; Validated; Region: PRK00378 1427342003572 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1427342003573 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1427342003574 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1427342003575 hydrophobic ligand binding site; other site 1427342003576 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1427342003577 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342003578 catalytic triad [active] 1427342003579 dimer interface [polypeptide binding]; other site 1427342003580 conserved cis-peptide bond; other site 1427342003581 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342003582 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342003583 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 1427342003584 dimerization interface [polypeptide binding]; other site 1427342003585 substrate binding pocket [chemical binding]; other site 1427342003586 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342003587 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1427342003588 C-terminal domain interface [polypeptide binding]; other site 1427342003589 GSH binding site (G-site) [chemical binding]; other site 1427342003590 dimer interface [polypeptide binding]; other site 1427342003591 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 1427342003592 dimer interface [polypeptide binding]; other site 1427342003593 N-terminal domain interface [polypeptide binding]; other site 1427342003594 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342003595 Tir chaperone protein (CesT) family; Region: CesT; pfam05932 1427342003596 NAD+--asparagine ADP-ribosyltransferase [Signal transduction mechanisms]; Region: COG5585 1427342003597 GTPase-activating protein (GAP) domain found in bacterial cytotoxins, ExoS, SptP, and YopE. Part of protein secretion system; stimulates Rac1- dependent cytoskeletal changes that promote bacterial internalization; Region: ToxGAP; cd00219 1427342003598 switch II binding region; other site 1427342003599 Rac1 P-loop interaction site [polypeptide binding]; other site 1427342003600 GTP binding residues [chemical binding]; other site 1427342003601 switch I binding region; other site 1427342003602 ADP-ribosyltransferase exoenzyme; Region: ADPrib_exo_Tox; pfam03496 1427342003603 active site 1427342003604 conformational flexibility of ligand binding pocket; other site 1427342003605 ADP-ribosylating toxin turn-turn motif; other site 1427342003606 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 1427342003607 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342003608 S-adenosylmethionine binding site [chemical binding]; other site 1427342003609 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 1427342003610 transmembrane helices; other site 1427342003611 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 1427342003612 TrkA-C domain; Region: TrkA_C; pfam02080 1427342003613 TrkA-C domain; Region: TrkA_C; pfam02080 1427342003614 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 1427342003615 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1427342003616 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342003617 Walker A/P-loop; other site 1427342003618 ATP binding site [chemical binding]; other site 1427342003619 Q-loop/lid; other site 1427342003620 ABC transporter signature motif; other site 1427342003621 Walker B; other site 1427342003622 D-loop; other site 1427342003623 H-loop/switch region; other site 1427342003624 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342003625 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 1427342003626 TM-ABC transporter signature motif; other site 1427342003627 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 1427342003628 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 1427342003629 zinc binding site [ion binding]; other site 1427342003630 putative ligand binding site [chemical binding]; other site 1427342003631 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 1427342003632 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1427342003633 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1427342003634 HIGH motif; other site 1427342003635 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1427342003636 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1427342003637 active site 1427342003638 KMSKS motif; other site 1427342003639 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1427342003640 tRNA binding surface [nucleotide binding]; other site 1427342003641 anticodon binding site; other site 1427342003642 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 1427342003643 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 1427342003644 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1427342003645 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 1427342003646 interface (dimer of trimers) [polypeptide binding]; other site 1427342003647 Substrate-binding/catalytic site; other site 1427342003648 Zn-binding sites [ion binding]; other site 1427342003649 Cupin domain; Region: Cupin_2; pfam07883 1427342003650 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342003651 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342003652 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342003653 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 1427342003654 Predicted permeases [General function prediction only]; Region: COG0795 1427342003655 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1427342003656 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1427342003657 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1427342003658 RDD family; Region: RDD; pfam06271 1427342003659 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 1427342003660 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 1427342003661 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342003662 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1427342003663 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1427342003664 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1427342003665 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1427342003666 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1427342003667 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 1427342003668 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1427342003669 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1427342003670 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1427342003671 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1427342003672 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1427342003673 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342003674 hypothetical protein; Provisional; Region: PRK11280 1427342003675 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1427342003676 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 1427342003677 active site 1427342003678 dimerization interface [polypeptide binding]; other site 1427342003679 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1427342003680 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1427342003681 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 1427342003682 serine O-acetyltransferase; Region: cysE; TIGR01172 1427342003683 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 1427342003684 trimer interface [polypeptide binding]; other site 1427342003685 active site 1427342003686 substrate binding site [chemical binding]; other site 1427342003687 CoA binding site [chemical binding]; other site 1427342003688 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1427342003689 Rrf2 family protein; Region: rrf2_super; TIGR00738 1427342003690 cysteine desulfurase; Provisional; Region: PRK14012 1427342003691 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1427342003692 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342003693 catalytic residue [active] 1427342003694 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1427342003695 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1427342003696 trimerization site [polypeptide binding]; other site 1427342003697 active site 1427342003698 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 1427342003699 co-chaperone HscB; Provisional; Region: hscB; PRK00294 1427342003700 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 1427342003701 HSP70 interaction site [polypeptide binding]; other site 1427342003702 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 1427342003703 chaperone protein HscA; Provisional; Region: hscA; PRK05183 1427342003704 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 1427342003705 nucleotide binding site [chemical binding]; other site 1427342003706 putative NEF/HSP70 interaction site [polypeptide binding]; other site 1427342003707 SBD interface [polypeptide binding]; other site 1427342003708 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1427342003709 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342003710 catalytic loop [active] 1427342003711 iron binding site [ion binding]; other site 1427342003712 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 1427342003713 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 1427342003714 active site 1427342003715 multimer interface [polypeptide binding]; other site 1427342003716 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 1427342003717 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342003718 FeS/SAM binding site; other site 1427342003719 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 1427342003720 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342003721 binding surface 1427342003722 TPR motif; other site 1427342003723 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342003724 binding surface 1427342003725 TPR motif; other site 1427342003726 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1427342003727 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342003728 non-specific DNA binding site [nucleotide binding]; other site 1427342003729 salt bridge; other site 1427342003730 sequence-specific DNA binding site [nucleotide binding]; other site 1427342003731 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 1427342003732 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 1427342003733 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1427342003734 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1427342003735 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1427342003736 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 1427342003737 dimer interface [polypeptide binding]; other site 1427342003738 motif 1; other site 1427342003739 active site 1427342003740 motif 2; other site 1427342003741 motif 3; other site 1427342003742 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 1427342003743 anticodon binding site; other site 1427342003744 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 1427342003745 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 1427342003746 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 1427342003747 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 1427342003748 Trp docking motif [polypeptide binding]; other site 1427342003749 active site 1427342003750 GTP-binding protein Der; Reviewed; Region: PRK00093 1427342003751 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1427342003752 G1 box; other site 1427342003753 GTP/Mg2+ binding site [chemical binding]; other site 1427342003754 Switch I region; other site 1427342003755 G2 box; other site 1427342003756 Switch II region; other site 1427342003757 G3 box; other site 1427342003758 G4 box; other site 1427342003759 G5 box; other site 1427342003760 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1427342003761 G1 box; other site 1427342003762 GTP/Mg2+ binding site [chemical binding]; other site 1427342003763 Switch I region; other site 1427342003764 G2 box; other site 1427342003765 G3 box; other site 1427342003766 Switch II region; other site 1427342003767 G4 box; other site 1427342003768 G5 box; other site 1427342003769 methionine aminotransferase; Validated; Region: PRK09082 1427342003770 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342003771 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342003772 homodimer interface [polypeptide binding]; other site 1427342003773 catalytic residue [active] 1427342003774 C-N hydrolase family amidase; Provisional; Region: PRK10438 1427342003775 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 1427342003776 putative active site [active] 1427342003777 catalytic triad [active] 1427342003778 dimer interface [polypeptide binding]; other site 1427342003779 multimer interface [polypeptide binding]; other site 1427342003780 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3753 1427342003781 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342003782 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342003783 active site 1427342003784 catalytic tetrad [active] 1427342003785 2-isopropylmalate synthase; Validated; Region: PRK03739 1427342003786 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 1427342003787 active site 1427342003788 catalytic residues [active] 1427342003789 metal binding site [ion binding]; metal-binding site 1427342003790 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 1427342003791 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 1427342003792 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342003793 N-terminal plug; other site 1427342003794 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 1427342003795 ligand-binding site [chemical binding]; other site 1427342003796 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342003797 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 1427342003798 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1427342003799 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342003800 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1427342003801 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1427342003802 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342003803 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 1427342003804 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1427342003805 AZL_007950 family protein; Region: AZL_007950_fam; TIGR04061 1427342003806 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342003807 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 1427342003808 catalytic triad [active] 1427342003809 conserved cis-peptide bond; other site 1427342003810 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 1427342003811 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 1427342003812 conserved cys residue [active] 1427342003813 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342003814 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 1427342003815 DctM-like transporters; Region: DctM; pfam06808 1427342003816 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 1427342003817 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 1427342003818 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 1427342003819 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 1427342003820 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342003821 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342003822 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342003823 dimerization interface [polypeptide binding]; other site 1427342003824 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1427342003825 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 1427342003826 generic binding surface II; other site 1427342003827 generic binding surface I; other site 1427342003828 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 1427342003829 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342003830 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342003831 dimerization interface [polypeptide binding]; other site 1427342003832 substrate binding pocket [chemical binding]; other site 1427342003833 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_1; cd09996 1427342003834 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 1427342003835 active site 1427342003836 Zn binding site [ion binding]; other site 1427342003837 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 1427342003838 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342003839 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342003840 DNA binding residues [nucleotide binding] 1427342003841 dimerization interface [polypeptide binding]; other site 1427342003842 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 1427342003843 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 1427342003844 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 1427342003845 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 1427342003846 active site 1427342003847 GMP synthase; Reviewed; Region: guaA; PRK00074 1427342003848 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 1427342003849 AMP/PPi binding site [chemical binding]; other site 1427342003850 candidate oxyanion hole; other site 1427342003851 catalytic triad [active] 1427342003852 potential glutamine specificity residues [chemical binding]; other site 1427342003853 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 1427342003854 ATP Binding subdomain [chemical binding]; other site 1427342003855 Dimerization subdomain; other site 1427342003856 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1427342003857 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 1427342003858 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 1427342003859 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 1427342003860 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 1427342003861 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 1427342003862 nucleoside/Zn binding site; other site 1427342003863 dimer interface [polypeptide binding]; other site 1427342003864 catalytic motif [active] 1427342003865 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 1427342003866 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1427342003867 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; pfam09998 1427342003868 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 1427342003869 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342003870 substrate binding pocket [chemical binding]; other site 1427342003871 membrane-bound complex binding site; other site 1427342003872 hinge residues; other site 1427342003873 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342003874 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342003875 catalytic residue [active] 1427342003876 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 1427342003877 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 1427342003878 dimerization interface [polypeptide binding]; other site 1427342003879 ATP binding site [chemical binding]; other site 1427342003880 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 1427342003881 dimerization interface [polypeptide binding]; other site 1427342003882 ATP binding site [chemical binding]; other site 1427342003883 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 1427342003884 putative active site [active] 1427342003885 catalytic triad [active] 1427342003886 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 1427342003887 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 1427342003888 Phosphotransferase system, EIIC; Region: PTS_EIIC; pfam02378 1427342003889 PTS system, glucose-like IIB component; Region: EIIB_glc; TIGR00826 1427342003890 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 1427342003891 active site turn [active] 1427342003892 phosphorylation site [posttranslational modification] 1427342003893 Phosphotransferase system IIA components [Carbohydrate transport and metabolism]; Region: NagE; COG2190 1427342003894 HPr interaction site; other site 1427342003895 glycerol kinase (GK) interaction site [polypeptide binding]; other site 1427342003896 active site 1427342003897 phosphorylation site [posttranslational modification] 1427342003898 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 1427342003899 regulatory protein interface [polypeptide binding]; other site 1427342003900 active site 1427342003901 regulatory phosphorylation site [posttranslational modification]; other site 1427342003902 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 1427342003903 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 1427342003904 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1427342003905 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1427342003906 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 1427342003907 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 1427342003908 dimer interface [polypeptide binding]; other site 1427342003909 active site 1427342003910 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 1427342003911 dimer interface [polypeptide binding]; other site 1427342003912 active site 1427342003913 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 1427342003914 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 1427342003915 active site 1427342003916 dimer interface [polypeptide binding]; other site 1427342003917 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 1427342003918 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342003919 DNA-binding site [nucleotide binding]; DNA binding site 1427342003920 UTRA domain; Region: UTRA; pfam07702 1427342003921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 1427342003922 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1427342003923 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 1427342003924 nudix motif; other site 1427342003925 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 1427342003926 putative active site [active] 1427342003927 putative CoA binding site [chemical binding]; other site 1427342003928 nudix motif; other site 1427342003929 metal binding site [ion binding]; metal-binding site 1427342003930 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1427342003931 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 1427342003932 trimer interface [polypeptide binding]; other site 1427342003933 putative metal binding site [ion binding]; other site 1427342003934 Predicted Fe-S protein [General function prediction only]; Region: COG3313 1427342003935 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 1427342003936 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342003937 ATP-grasp domain; Region: ATP-grasp; pfam02222 1427342003938 SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it...; Region: FeeA_FeeB_like; cd01836 1427342003939 active site 1427342003940 catalytic triad [active] 1427342003941 oxyanion hole [active] 1427342003942 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342003943 metabolite-proton symporter; Region: 2A0106; TIGR00883 1427342003944 putative substrate translocation pore; other site 1427342003945 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1427342003946 Domain of unknown function DUF21; Region: DUF21; pfam01595 1427342003947 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 1427342003948 Transporter associated domain; Region: CorC_HlyC; smart01091 1427342003949 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4137 1427342003950 signal recognition particle protein; Provisional; Region: PRK10867 1427342003951 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1427342003952 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 1427342003953 P loop; other site 1427342003954 GTP binding site [chemical binding]; other site 1427342003955 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1427342003956 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1427342003957 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1427342003958 RimM N-terminal domain; Region: RimM; pfam01782 1427342003959 PRC-barrel domain; Region: PRC; pfam05239 1427342003960 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 1427342003961 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1427342003962 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 1427342003963 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 1427342003964 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1427342003965 TrkA-N domain; Region: TrkA_N; pfam02254 1427342003966 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1427342003967 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 1427342003968 active site 1427342003969 Int/Topo IB signature motif; other site 1427342003970 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 1427342003971 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 1427342003972 dimerization domain [polypeptide binding]; other site 1427342003973 dimer interface [polypeptide binding]; other site 1427342003974 catalytic residues [active] 1427342003975 homoserine dehydrogenase; Provisional; Region: PRK06349 1427342003976 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 1427342003977 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 1427342003978 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 1427342003979 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 1427342003980 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 1427342003981 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342003982 catalytic residue [active] 1427342003983 Chlorophyllase enzyme; Region: Chlorophyllase2; pfam12740 1427342003984 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 1427342003985 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1427342003986 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1427342003987 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 1427342003988 nucleotide binding site [chemical binding]; other site 1427342003989 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3789 1427342003990 PspA/IM30 family; Region: PspA_IM30; pfam04012 1427342003991 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 1427342003992 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 1427342003993 ATPase involved in DNA repair; Region: DUF3686; pfam12458 1427342003994 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cl02488 1427342003995 linker region; other site 1427342003996 AAA domain; Region: AAA_22; pfam13401 1427342003997 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342003998 Walker A motif; other site 1427342003999 ATP binding site [chemical binding]; other site 1427342004000 Walker B motif; other site 1427342004001 Catalytic domain of vertebrate phospholipase D6 and similar proteins; Region: PLDc_vPLD6_like; cd09171 1427342004002 PLD-like domain; Region: PLDc_2; pfam13091 1427342004003 putative active site [active] 1427342004004 catalytic site [active] 1427342004005 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4681 1427342004006 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 1427342004007 DHH family; Region: DHH; pfam01368 1427342004008 DHHA1 domain; Region: DHHA1; pfam02272 1427342004009 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 1427342004010 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 1427342004011 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1427342004012 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 1427342004013 active site 1427342004014 Zn binding site [ion binding]; other site 1427342004015 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342004016 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 1427342004017 active site 1427342004018 FMN binding site [chemical binding]; other site 1427342004019 substrate binding site [chemical binding]; other site 1427342004020 homotetramer interface [polypeptide binding]; other site 1427342004021 catalytic residue [active] 1427342004022 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342004023 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342004024 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004025 putative substrate translocation pore; other site 1427342004026 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342004027 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 1427342004028 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342004029 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342004030 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004031 active site 1427342004032 phosphorylation site [posttranslational modification] 1427342004033 intermolecular recognition site; other site 1427342004034 dimerization interface [polypeptide binding]; other site 1427342004035 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004036 DNA binding residues [nucleotide binding] 1427342004037 dimerization interface [polypeptide binding]; other site 1427342004038 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342004039 Protein of unknown function (DUF533); Region: DUF533; pfam04391 1427342004040 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 1427342004041 putative metal binding site [ion binding]; other site 1427342004042 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342004043 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004044 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342004045 dimerization interface [polypeptide binding]; other site 1427342004046 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 1427342004047 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342004048 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004049 putative substrate translocation pore; other site 1427342004050 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1427342004051 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342004052 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342004053 dimerization interface [polypeptide binding]; other site 1427342004054 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342004055 dimer interface [polypeptide binding]; other site 1427342004056 putative CheW interface [polypeptide binding]; other site 1427342004057 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1427342004058 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 1427342004059 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342004060 S-adenosylmethionine binding site [chemical binding]; other site 1427342004061 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1427342004062 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342004063 putative binding surface; other site 1427342004064 active site 1427342004065 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1427342004066 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342004067 ATP binding site [chemical binding]; other site 1427342004068 Mg2+ binding site [ion binding]; other site 1427342004069 G-X-G motif; other site 1427342004070 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 1427342004071 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342004072 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004073 active site 1427342004074 phosphorylation site [posttranslational modification] 1427342004075 intermolecular recognition site; other site 1427342004076 dimerization interface [polypeptide binding]; other site 1427342004077 chemotaxis-specific methylesterase; Provisional; Region: PRK12555 1427342004078 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004079 phosphorylation site [posttranslational modification] 1427342004080 intermolecular recognition site; other site 1427342004081 CheB methylesterase; Region: CheB_methylest; pfam01339 1427342004082 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342004083 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004084 active site 1427342004085 phosphorylation site [posttranslational modification] 1427342004086 intermolecular recognition site; other site 1427342004087 dimerization interface [polypeptide binding]; other site 1427342004088 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342004089 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342004090 metal binding site [ion binding]; metal-binding site 1427342004091 active site 1427342004092 I-site; other site 1427342004093 peptide chain release factor 2; Provisional; Region: PRK08787 1427342004094 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1427342004095 RF-1 domain; Region: RF-1; pfam00472 1427342004096 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 1427342004097 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 1427342004098 dimer interface [polypeptide binding]; other site 1427342004099 putative anticodon binding site; other site 1427342004100 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 1427342004101 motif 1; other site 1427342004102 active site 1427342004103 motif 2; other site 1427342004104 motif 3; other site 1427342004105 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3226 1427342004106 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3930 1427342004107 Uncharacterized conserved protein [Function unknown]; Region: COG2013 1427342004108 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 1427342004109 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342004110 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342004111 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342004112 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 1427342004113 putative ADP-ribose binding site [chemical binding]; other site 1427342004114 putative active site [active] 1427342004115 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342004116 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342004117 ligand binding site [chemical binding]; other site 1427342004118 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 1427342004119 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1427342004120 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 1427342004121 metal-binding site [ion binding] 1427342004122 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342004123 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1427342004124 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 1427342004125 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 1427342004126 DNA binding residues [nucleotide binding] 1427342004127 dimer interface [polypeptide binding]; other site 1427342004128 putative metal binding site [ion binding]; other site 1427342004129 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 1427342004130 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 1427342004131 adenylate kinase; Reviewed; Region: adk; PRK00279 1427342004132 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 1427342004133 AMP-binding site [chemical binding]; other site 1427342004134 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1427342004135 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1427342004136 Glycoprotease family; Region: Peptidase_M22; pfam00814 1427342004137 Protein of unknown function DUF72; Region: DUF72; cl00777 1427342004138 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 1427342004139 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 1427342004140 tetramer interface [polypeptide binding]; other site 1427342004141 active site 1427342004142 Mg2+/Mn2+ binding site [ion binding]; other site 1427342004143 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 1427342004144 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342004145 S-adenosylmethionine binding site [chemical binding]; other site 1427342004146 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 1427342004147 Cytochrome P450; Region: p450; cl12078 1427342004148 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342004149 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342004150 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 1427342004151 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342004152 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342004153 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342004154 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1427342004155 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 1427342004156 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 1427342004157 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 1427342004158 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 1427342004159 putative acyl-acceptor binding pocket; other site 1427342004160 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1427342004161 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1427342004162 Walker A/P-loop; other site 1427342004163 ATP binding site [chemical binding]; other site 1427342004164 Q-loop/lid; other site 1427342004165 ABC transporter signature motif; other site 1427342004166 Walker B; other site 1427342004167 D-loop; other site 1427342004168 H-loop/switch region; other site 1427342004169 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 1427342004170 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 1427342004171 ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility and secretion]; Region: GldG; COG3225 1427342004172 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 1427342004173 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 1427342004174 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1427342004175 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 1427342004176 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342004177 catalytic residue [active] 1427342004178 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Region: DapD_gpp; TIGR03536 1427342004179 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 1427342004180 putative trimer interface [polypeptide binding]; other site 1427342004181 putative CoA binding site [chemical binding]; other site 1427342004182 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342004183 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 1427342004184 ArsC family; Region: ArsC; pfam03960 1427342004185 putative catalytic residues [active] 1427342004186 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 1427342004187 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342004188 Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the superfamily...; Region: INT_Lambda_C; cd00800 1427342004189 dimer interface [polypeptide binding]; other site 1427342004190 active site 1427342004191 Int/Topo IB signature motif; other site 1427342004192 Protein of unknown function (DUF550); Region: DUF550; pfam04447 1427342004193 Domain of unknown function (DUF4406); Region: DUF4406; pfam14359 1427342004194 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1427342004195 DNA methylase; Region: N6_N4_Mtase; cl17433 1427342004196 DNA methylase; Region: N6_N4_Mtase; cl17433 1427342004197 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1427342004198 DNA methylase; Region: N6_N4_Mtase; pfam01555 1427342004199 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cl17512 1427342004200 beta-clamp/clamp loader binding surface; other site 1427342004201 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004202 DNA binding residues [nucleotide binding] 1427342004203 dimerization interface [polypeptide binding]; other site 1427342004204 ParB-like nuclease domain; Region: ParBc; pfam02195 1427342004205 KorB domain; Region: KorB; pfam08535 1427342004206 Predicted transcriptional regulator [Transcription]; Region: COG2932 1427342004207 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1427342004208 Catalytic site [active] 1427342004209 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 1427342004210 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 1427342004211 Phage-related protein [Function unknown]; Region: COG4695 1427342004212 Phage portal protein; Region: Phage_portal; pfam04860 1427342004213 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 1427342004214 oligomer interface [polypeptide binding]; other site 1427342004215 Clp protease; Region: CLP_protease; pfam00574 1427342004216 active site residues [active] 1427342004217 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 1427342004218 Phage capsid family; Region: Phage_capsid; pfam05065 1427342004219 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 1427342004220 oligomerization interface [polypeptide binding]; other site 1427342004221 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 1427342004222 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1427342004223 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 1427342004224 Gas vesicle protein G; Region: GvpG; pfam05120 1427342004225 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 1427342004226 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 1427342004227 Right handed beta helix region; Region: Beta_helix; pfam13229 1427342004228 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1427342004229 Predicted chitinase [General function prediction only]; Region: COG3179 1427342004230 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1427342004231 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 1427342004232 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1427342004233 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 1427342004234 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342004235 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342004236 homodimer interface [polypeptide binding]; other site 1427342004237 catalytic residue [active] 1427342004238 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 1427342004239 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 1427342004240 metal binding triad; other site 1427342004241 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 1427342004242 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342004243 Zn2+ binding site [ion binding]; other site 1427342004244 Mg2+ binding site [ion binding]; other site 1427342004245 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 1427342004246 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 1427342004247 methionine aminopeptidase; Provisional; Region: PRK08671 1427342004248 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 1427342004249 active site 1427342004250 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 1427342004251 rRNA interaction site [nucleotide binding]; other site 1427342004252 S8 interaction site; other site 1427342004253 putative laminin-1 binding site; other site 1427342004254 elongation factor Ts; Provisional; Region: tsf; PRK09377 1427342004255 UBA/TS-N domain; Region: UBA; pfam00627 1427342004256 Elongation factor TS; Region: EF_TS; pfam00889 1427342004257 Elongation factor TS; Region: EF_TS; pfam00889 1427342004258 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 1427342004259 putative nucleotide binding site [chemical binding]; other site 1427342004260 uridine monophosphate binding site [chemical binding]; other site 1427342004261 homohexameric interface [polypeptide binding]; other site 1427342004262 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1427342004263 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 1427342004264 hinge region; other site 1427342004265 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 1427342004266 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 1427342004267 catalytic residue [active] 1427342004268 putative FPP diphosphate binding site; other site 1427342004269 putative FPP binding hydrophobic cleft; other site 1427342004270 dimer interface [polypeptide binding]; other site 1427342004271 putative IPP diphosphate binding site; other site 1427342004272 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 1427342004273 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1427342004274 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 1427342004275 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 1427342004276 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 1427342004277 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 1427342004278 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 1427342004279 zinc metallopeptidase RseP; Provisional; Region: PRK10779 1427342004280 active site 1427342004281 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 1427342004282 protein binding site [polypeptide binding]; other site 1427342004283 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 1427342004284 protein binding site [polypeptide binding]; other site 1427342004285 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 1427342004286 putative substrate binding region [chemical binding]; other site 1427342004287 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 1427342004288 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342004289 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342004290 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342004291 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342004292 Surface antigen; Region: Bac_surface_Ag; pfam01103 1427342004293 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1427342004294 periplasmic chaperone; Provisional; Region: PRK10780 1427342004295 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1427342004296 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1427342004297 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 1427342004298 trimer interface [polypeptide binding]; other site 1427342004299 active site 1427342004300 UDP-GlcNAc binding site [chemical binding]; other site 1427342004301 lipid binding site [chemical binding]; lipid-binding site 1427342004302 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 1427342004303 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 1427342004304 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 1427342004305 active site 1427342004306 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1427342004307 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1427342004308 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1427342004309 RNA/DNA hybrid binding site [nucleotide binding]; other site 1427342004310 active site 1427342004311 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1427342004312 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 1427342004313 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1427342004314 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1427342004315 putative active site [active] 1427342004316 putative PHP Thumb interface [polypeptide binding]; other site 1427342004317 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 1427342004318 generic binding surface II; other site 1427342004319 generic binding surface I; other site 1427342004320 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 1427342004321 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 1427342004322 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 1427342004323 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 1427342004324 Ligand Binding Site [chemical binding]; other site 1427342004325 TilS substrate binding domain; Region: TilS; pfam09179 1427342004326 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 1427342004327 CTP synthetase; Validated; Region: pyrG; PRK05380 1427342004328 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 1427342004329 Catalytic site [active] 1427342004330 active site 1427342004331 UTP binding site [chemical binding]; other site 1427342004332 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1427342004333 active site 1427342004334 putative oxyanion hole; other site 1427342004335 catalytic triad [active] 1427342004336 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 1427342004337 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1427342004338 enolase; Provisional; Region: eno; PRK00077 1427342004339 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 1427342004340 dimer interface [polypeptide binding]; other site 1427342004341 metal binding site [ion binding]; metal-binding site 1427342004342 substrate binding pocket [chemical binding]; other site 1427342004343 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1427342004344 Septum formation initiator; Region: DivIC; cl17659 1427342004345 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 1427342004346 substrate binding site; other site 1427342004347 dimer interface; other site 1427342004348 YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system...; Region: YedF; cd03422 1427342004349 CPxP motif; other site 1427342004350 putative inner membrane protein; Provisional; Region: PRK11099 1427342004351 Sulphur transport; Region: Sulf_transp; pfam04143 1427342004352 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342004353 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004354 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 1427342004355 putative effector binding pocket; other site 1427342004356 putative dimerization interface [polypeptide binding]; other site 1427342004357 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 1427342004358 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 1427342004359 substrate binding site [chemical binding]; other site 1427342004360 catalytic Zn binding site [ion binding]; other site 1427342004361 NAD binding site [chemical binding]; other site 1427342004362 structural Zn binding site [ion binding]; other site 1427342004363 dimer interface [polypeptide binding]; other site 1427342004364 S-formylglutathione hydrolase; Region: PLN02442 1427342004365 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 1427342004366 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 1427342004367 homotrimer interaction site [polypeptide binding]; other site 1427342004368 zinc binding site [ion binding]; other site 1427342004369 CDP-binding sites; other site 1427342004370 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 1427342004371 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 1427342004372 Permutation of conserved domain; other site 1427342004373 active site 1427342004374 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1427342004375 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 1427342004376 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 1427342004377 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342004378 S-adenosylmethionine binding site [chemical binding]; other site 1427342004379 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342004380 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 1427342004381 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1427342004382 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342004383 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1427342004384 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342004385 DNA binding residues [nucleotide binding] 1427342004386 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1427342004387 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 1427342004388 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1427342004389 MutS domain I; Region: MutS_I; pfam01624 1427342004390 MutS domain II; Region: MutS_II; pfam05188 1427342004391 MutS domain III; Region: MutS_III; pfam05192 1427342004392 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1427342004393 Walker A/P-loop; other site 1427342004394 ATP binding site [chemical binding]; other site 1427342004395 Q-loop/lid; other site 1427342004396 ABC transporter signature motif; other site 1427342004397 Walker B; other site 1427342004398 D-loop; other site 1427342004399 H-loop/switch region; other site 1427342004400 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 1427342004401 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 1427342004402 recombinase A; Provisional; Region: recA; PRK09354 1427342004403 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 1427342004404 hexamer interface [polypeptide binding]; other site 1427342004405 Walker A motif; other site 1427342004406 ATP binding site [chemical binding]; other site 1427342004407 Walker B motif; other site 1427342004408 recombination regulator RecX; Reviewed; Region: recX; PRK00117 1427342004409 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 1427342004410 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 1427342004411 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342004412 Beta-Casp domain; Region: Beta-Casp; smart01027 1427342004413 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1427342004414 Phosphoketolase [Carbohydrate transport and metabolism]; Region: COG3957 1427342004415 XFP N-terminal domain; Region: XFP_N; pfam09364 1427342004416 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3530 1427342004417 Domain of unknown function (DUF4146); Region: DUF4146; pfam13652 1427342004418 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342004419 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342004420 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342004421 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342004422 dimer interface [polypeptide binding]; other site 1427342004423 conserved gate region; other site 1427342004424 putative PBP binding loops; other site 1427342004425 ABC-ATPase subunit interface; other site 1427342004426 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342004427 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342004428 dimer interface [polypeptide binding]; other site 1427342004429 conserved gate region; other site 1427342004430 putative PBP binding loops; other site 1427342004431 ABC-ATPase subunit interface; other site 1427342004432 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1427342004433 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342004434 Walker A/P-loop; other site 1427342004435 ATP binding site [chemical binding]; other site 1427342004436 Q-loop/lid; other site 1427342004437 ABC transporter signature motif; other site 1427342004438 Walker B; other site 1427342004439 D-loop; other site 1427342004440 H-loop/switch region; other site 1427342004441 TOBE domain; Region: TOBE_2; pfam08402 1427342004442 Uncharacterized conserved protein [Function unknown]; Region: COG3148 1427342004443 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1427342004444 EamA-like transporter family; Region: EamA; pfam00892 1427342004445 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342004446 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004447 active site 1427342004448 phosphorylation site [posttranslational modification] 1427342004449 intermolecular recognition site; other site 1427342004450 dimerization interface [polypeptide binding]; other site 1427342004451 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004452 DNA binding residues [nucleotide binding] 1427342004453 dimerization interface [polypeptide binding]; other site 1427342004454 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 1427342004455 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 1427342004456 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 1427342004457 active site 1427342004458 FMN binding site [chemical binding]; other site 1427342004459 substrate binding site [chemical binding]; other site 1427342004460 3Fe-4S cluster binding site [ion binding]; other site 1427342004461 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 1427342004462 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1427342004463 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342004464 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004465 DNA binding residues [nucleotide binding] 1427342004466 dimerization interface [polypeptide binding]; other site 1427342004467 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1427342004468 Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases); Region: R-amidase_like; cd07576 1427342004469 putative active site [active] 1427342004470 catalytic triad [active] 1427342004471 putative dimer interface [polypeptide binding]; other site 1427342004472 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342004473 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1427342004474 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1427342004475 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1427342004476 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1427342004477 DNA binding site [nucleotide binding] 1427342004478 active site 1427342004479 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004480 metabolite-proton symporter; Region: 2A0106; TIGR00883 1427342004481 putative substrate translocation pore; other site 1427342004482 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342004483 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004484 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like_2; cd08448 1427342004485 putative dimerization interface [polypeptide binding]; other site 1427342004486 putative substrate binding pocket [chemical binding]; other site 1427342004487 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342004488 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 1427342004489 active site 1427342004490 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1427342004491 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1427342004492 enoyl-CoA hydratase; Provisional; Region: PRK08138 1427342004493 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342004494 substrate binding site [chemical binding]; other site 1427342004495 oxyanion hole (OAH) forming residues; other site 1427342004496 trimer interface [polypeptide binding]; other site 1427342004497 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 1427342004498 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342004499 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342004500 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342004501 acetyl-CoA acetyltransferase; Provisional; Region: PRK08131 1427342004502 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342004503 dimer interface [polypeptide binding]; other site 1427342004504 active site 1427342004505 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342004506 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 1427342004507 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004508 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 1427342004509 putative dimerization interface [polypeptide binding]; other site 1427342004510 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342004511 GlpM protein; Region: GlpM; pfam06942 1427342004512 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 1427342004513 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 1427342004514 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 1427342004515 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 1427342004516 glycerol kinase; Provisional; Region: glpK; PRK00047 1427342004517 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 1427342004518 N- and C-terminal domain interface [polypeptide binding]; other site 1427342004519 active site 1427342004520 MgATP binding site [chemical binding]; other site 1427342004521 catalytic site [active] 1427342004522 metal binding site [ion binding]; metal-binding site 1427342004523 glycerol binding site [chemical binding]; other site 1427342004524 homotetramer interface [polypeptide binding]; other site 1427342004525 homodimer interface [polypeptide binding]; other site 1427342004526 FBP binding site [chemical binding]; other site 1427342004527 protein IIAGlc interface [polypeptide binding]; other site 1427342004528 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 1427342004529 amphipathic channel; other site 1427342004530 Asn-Pro-Ala signature motifs; other site 1427342004531 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 1427342004532 putative deacylase active site [active] 1427342004533 glycerol kinase; Region: glycerol_kin; TIGR01311 1427342004534 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 1427342004535 N- and C-terminal domain interface [polypeptide binding]; other site 1427342004536 active site 1427342004537 MgATP binding site [chemical binding]; other site 1427342004538 catalytic site [active] 1427342004539 metal binding site [ion binding]; metal-binding site 1427342004540 glycerol binding site [chemical binding]; other site 1427342004541 homotetramer interface [polypeptide binding]; other site 1427342004542 homodimer interface [polypeptide binding]; other site 1427342004543 FBP binding site [chemical binding]; other site 1427342004544 protein IIAGlc interface [polypeptide binding]; other site 1427342004545 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 1427342004546 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1427342004547 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342004548 metal-binding site [ion binding] 1427342004549 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 1427342004550 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342004551 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 1427342004552 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004553 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 1427342004554 putative substrate translocation pore; other site 1427342004555 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342004556 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342004557 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342004558 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 1427342004559 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 1427342004560 tetrameric interface [polypeptide binding]; other site 1427342004561 NAD binding site [chemical binding]; other site 1427342004562 catalytic residues [active] 1427342004563 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1427342004564 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 1427342004565 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 1427342004566 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 1427342004567 acyl-activating enzyme (AAE) consensus motif; other site 1427342004568 putative AMP binding site [chemical binding]; other site 1427342004569 putative active site [active] 1427342004570 putative CoA binding site [chemical binding]; other site 1427342004571 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 1427342004572 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 1427342004573 putative NAD(P) binding site [chemical binding]; other site 1427342004574 dimer interface [polypeptide binding]; other site 1427342004575 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342004576 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342004577 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004578 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342004579 putative effector binding pocket; other site 1427342004580 dimerization interface [polypeptide binding]; other site 1427342004581 Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the...; Region: Barstar_like; cl01048 1427342004582 RNAase interaction site [polypeptide binding]; other site 1427342004583 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1427342004584 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1427342004585 active site 1427342004586 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 1427342004587 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1427342004588 DNA binding site [nucleotide binding] 1427342004589 domain linker motif; other site 1427342004590 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 1427342004591 dimerization interface [polypeptide binding]; other site 1427342004592 ligand binding site [chemical binding]; other site 1427342004593 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 1427342004594 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 1427342004595 active site 1427342004596 phosphorylation site [posttranslational modification] 1427342004597 Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2; Region: PTS_EIIA_2; pfam00359 1427342004598 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 1427342004599 dimerization domain swap beta strand [polypeptide binding]; other site 1427342004600 regulatory protein interface [polypeptide binding]; other site 1427342004601 active site 1427342004602 regulatory phosphorylation site [posttranslational modification]; other site 1427342004603 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 1427342004604 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 1427342004605 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1427342004606 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1427342004607 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 1427342004608 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 1427342004609 putative substrate binding site [chemical binding]; other site 1427342004610 putative ATP binding site [chemical binding]; other site 1427342004611 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 1427342004612 active site 1427342004613 P-loop; other site 1427342004614 phosphorylation site [posttranslational modification] 1427342004615 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 1427342004616 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 1427342004617 active site 1427342004618 P-loop; other site 1427342004619 phosphorylation site [posttranslational modification] 1427342004620 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 1427342004621 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1427342004622 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1427342004623 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1427342004624 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 1427342004625 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional; Region: PRK02971 1427342004626 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional; Region: PRK15051 1427342004627 4-amino-4-deoxy-L-arabinose transferase; Provisional; Region: arnT; PRK13279 1427342004628 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 1427342004629 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 1427342004630 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1427342004631 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1427342004632 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated; Region: PRK08125 1427342004633 active site 1427342004634 substrate binding site [chemical binding]; other site 1427342004635 cosubstrate binding site; other site 1427342004636 catalytic site [active] 1427342004637 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 1427342004638 active site 1427342004639 hexamer interface [polypeptide binding]; other site 1427342004640 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 1427342004641 NAD binding site [chemical binding]; other site 1427342004642 substrate binding site [chemical binding]; other site 1427342004643 active site 1427342004644 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 1427342004645 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 1427342004646 Ligand binding site; other site 1427342004647 Putative Catalytic site; other site 1427342004648 DXD motif; other site 1427342004649 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1427342004650 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 1427342004651 inhibitor-cofactor binding pocket; inhibition site 1427342004652 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342004653 catalytic residue [active] 1427342004654 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1427342004655 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1427342004656 Substrate binding site; other site 1427342004657 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 1427342004658 Alginate O-acetyl transferase AlgF; Region: AlgF; pfam11182 1427342004659 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 1427342004660 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cd00244 1427342004661 active site 1427342004662 Right handed beta helix region; Region: Beta_helix; pfam13229 1427342004663 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 1427342004664 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1427342004665 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1427342004666 Sel1-like repeats; Region: SEL1; smart00671 1427342004667 PilZ domain; Region: PilZ; pfam07238 1427342004668 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342004669 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342004670 active site 1427342004671 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 1427342004672 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1427342004673 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1427342004674 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 1427342004675 hypothetical protein; Validated; Region: PRK02101 1427342004676 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1427342004677 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 1427342004678 Walker A/P-loop; other site 1427342004679 ATP binding site [chemical binding]; other site 1427342004680 Q-loop/lid; other site 1427342004681 ABC transporter signature motif; other site 1427342004682 Walker B; other site 1427342004683 D-loop; other site 1427342004684 H-loop/switch region; other site 1427342004685 TOBE domain; Region: TOBE_2; pfam08402 1427342004686 ornithine carbamoyltransferase; Provisional; Region: PRK00779 1427342004687 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1427342004688 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1427342004689 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 1427342004690 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 1427342004691 catalytic triad [active] 1427342004692 putative active site [active] 1427342004693 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 1427342004694 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1427342004695 Autotransporter beta-domain; Region: Autotransporter; smart00869 1427342004696 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 1427342004697 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_1; cd02762 1427342004698 putative [Fe4-S4] binding site [ion binding]; other site 1427342004699 putative molybdopterin cofactor binding site [chemical binding]; other site 1427342004700 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_1; cd02782 1427342004701 putative molybdopterin cofactor binding site; other site 1427342004702 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 1427342004703 putative GSH binding site [chemical binding]; other site 1427342004704 catalytic residues [active] 1427342004705 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 1427342004706 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 1427342004707 heme binding site [chemical binding]; other site 1427342004708 ferroxidase pore; other site 1427342004709 ferroxidase diiron center [ion binding]; other site 1427342004710 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 1427342004711 peroxidase; Provisional; Region: PRK15000 1427342004712 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 1427342004713 dimer interface [polypeptide binding]; other site 1427342004714 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1427342004715 catalytic triad [active] 1427342004716 peroxidatic and resolving cysteines [active] 1427342004717 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 1427342004718 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 1427342004719 dimer interface [polypeptide binding]; other site 1427342004720 catalytic site [active] 1427342004721 putative active site [active] 1427342004722 putative substrate binding site [chemical binding]; other site 1427342004723 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 1427342004724 active site 1427342004725 substrate binding pocket [chemical binding]; other site 1427342004726 dimer interface [polypeptide binding]; other site 1427342004727 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342004728 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342004729 ligand binding site [chemical binding]; other site 1427342004730 argininosuccinate synthase; Provisional; Region: PRK13820 1427342004731 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 1427342004732 ANP binding site [chemical binding]; other site 1427342004733 Substrate Binding Site II [chemical binding]; other site 1427342004734 Substrate Binding Site I [chemical binding]; other site 1427342004735 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342004736 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 1427342004737 dimer interface [polypeptide binding]; other site 1427342004738 active site 1427342004739 metal binding site [ion binding]; metal-binding site 1427342004740 glutathione binding site [chemical binding]; other site 1427342004741 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342004742 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342004743 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342004744 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1427342004745 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342004746 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342004747 metal-binding site [ion binding] 1427342004748 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1427342004749 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 1427342004750 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 1427342004751 tetramer interface [polypeptide binding]; other site 1427342004752 active site 1427342004753 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 1427342004754 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 1427342004755 tetramer interface [polypeptide binding]; other site 1427342004756 active site 1427342004757 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342004758 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342004759 S-adenosylmethionine binding site [chemical binding]; other site 1427342004760 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1427342004761 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1427342004762 minor groove reading motif; other site 1427342004763 helix-hairpin-helix signature motif; other site 1427342004764 substrate binding pocket [chemical binding]; other site 1427342004765 active site 1427342004766 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1427342004767 electron transport complex RsxE subunit; Provisional; Region: PRK12405 1427342004768 Predicted NADH:ubiquinone oxidoreductase, subunit RnfG [Energy production and conversion]; Region: RnfG; COG4659 1427342004769 electron transport complex, RnfABCDGE type, D subunit; Region: rnfD; TIGR01946 1427342004770 electron transport complex protein RnfC; Provisional; Region: PRK05035 1427342004771 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 1427342004772 SLBB domain; Region: SLBB; pfam10531 1427342004773 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 1427342004774 electron transport complex protein RnfB; Provisional; Region: PRK05113 1427342004775 Putative Fe-S cluster; Region: FeS; pfam04060 1427342004776 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1427342004777 electron transport complex protein RsxA; Provisional; Region: PRK05151 1427342004778 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 1427342004779 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 1427342004780 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1427342004781 active site 1427342004782 HIGH motif; other site 1427342004783 KMSKS motif; other site 1427342004784 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1427342004785 tRNA binding surface [nucleotide binding]; other site 1427342004786 anticodon binding site; other site 1427342004787 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 1427342004788 putative tRNA-binding site [nucleotide binding]; other site 1427342004789 dimer interface [polypeptide binding]; other site 1427342004790 antiporter inner membrane protein; Provisional; Region: PRK11670 1427342004791 Domain of unknown function DUF59; Region: DUF59; pfam01883 1427342004792 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 1427342004793 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1427342004794 trimer interface [polypeptide binding]; other site 1427342004795 active site 1427342004796 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342004797 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 1427342004798 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 1427342004799 homodimer interface [polypeptide binding]; other site 1427342004800 active site 1427342004801 TDP-binding site; other site 1427342004802 acceptor substrate-binding pocket; other site 1427342004803 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 1427342004804 Autoinducer binding domain; Region: Autoind_bind; pfam03472 1427342004805 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004806 DNA binding residues [nucleotide binding] 1427342004807 dimerization interface [polypeptide binding]; other site 1427342004808 N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: LasI; COG3916 1427342004809 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1427342004810 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342004811 substrate binding pocket [chemical binding]; other site 1427342004812 membrane-bound complex binding site; other site 1427342004813 hinge residues; other site 1427342004814 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1427342004815 Predicted permeases [General function prediction only]; Region: RarD; COG2962 1427342004816 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 1427342004817 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1427342004818 NlpC/P60 family; Region: NLPC_P60; pfam00877 1427342004819 malate dehydrogenase; Provisional; Region: PRK13529 1427342004820 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1427342004821 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 1427342004822 NAD(P) binding site [chemical binding]; other site 1427342004823 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 1427342004824 nudix motif; other site 1427342004825 RibD C-terminal domain; Region: RibD_C; cl17279 1427342004826 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1427342004827 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1427342004828 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342004829 benzoate transport; Region: 2A0115; TIGR00895 1427342004830 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004831 putative substrate translocation pore; other site 1427342004832 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004833 helicase 45; Provisional; Region: PTZ00424 1427342004834 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342004835 ATP binding site [chemical binding]; other site 1427342004836 Mg++ binding site [ion binding]; other site 1427342004837 motif III; other site 1427342004838 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342004839 nucleotide binding region [chemical binding]; other site 1427342004840 ATP-binding site [chemical binding]; other site 1427342004841 Transmembrane secretion effector; Region: MFS_3; pfam05977 1427342004842 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342004843 putative substrate translocation pore; other site 1427342004844 Zinc dependent phospholipase C/S1-P1 nuclease; Region: ZnPC_S1P1; cl16915 1427342004845 hypothetical protein; Provisional; Region: PRK00304 1427342004846 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 1427342004847 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 1427342004848 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 1427342004849 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342004850 dimer interface [polypeptide binding]; other site 1427342004851 phosphorylation site [posttranslational modification] 1427342004852 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342004853 ATP binding site [chemical binding]; other site 1427342004854 Mg2+ binding site [ion binding]; other site 1427342004855 G-X-G motif; other site 1427342004856 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342004857 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342004858 active site 1427342004859 phosphorylation site [posttranslational modification] 1427342004860 intermolecular recognition site; other site 1427342004861 dimerization interface [polypeptide binding]; other site 1427342004862 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 1427342004863 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 1427342004864 putative oligomer interface [polypeptide binding]; other site 1427342004865 putative active site [active] 1427342004866 metal binding site [ion binding]; metal-binding site 1427342004867 GNAT-family acetyltransferase TIGR03103; Region: trio_acet_GNAT 1427342004868 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342004869 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342004870 asparagine synthase family amidotransferase; Region: trio_amidotrans; TIGR03104 1427342004871 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 1427342004872 active site 1427342004873 dimer interface [polypeptide binding]; other site 1427342004874 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 1427342004875 Ligand Binding Site [chemical binding]; other site 1427342004876 Molecular Tunnel; other site 1427342004877 MarR family; Region: MarR_2; cl17246 1427342004878 Predicted permeases [General function prediction only]; Region: COG0730 1427342004879 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 1427342004880 Uncharacterized conserved protein [Function unknown]; Region: COG4121 1427342004881 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 1427342004882 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 1427342004883 Uncharacterized conserved protein [Function unknown]; Region: COG2326 1427342004884 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 1427342004885 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342004886 dimer interface [polypeptide binding]; other site 1427342004887 active site 1427342004888 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3132 1427342004889 malate:quinone oxidoreductase; Validated; Region: PRK05257 1427342004890 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 1427342004891 Predicted periplasmic protein (DUF2092); Region: DUF2092; cl17607 1427342004892 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1427342004893 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 1427342004894 dimer interface [polypeptide binding]; other site 1427342004895 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1427342004896 catalytic triad [active] 1427342004897 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342004898 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342004899 substrate binding pocket [chemical binding]; other site 1427342004900 membrane-bound complex binding site; other site 1427342004901 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342004902 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342004903 dimer interface [polypeptide binding]; other site 1427342004904 conserved gate region; other site 1427342004905 putative PBP binding loops; other site 1427342004906 ABC-ATPase subunit interface; other site 1427342004907 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1427342004908 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342004909 Walker A/P-loop; other site 1427342004910 ATP binding site [chemical binding]; other site 1427342004911 Q-loop/lid; other site 1427342004912 ABC transporter signature motif; other site 1427342004913 Walker B; other site 1427342004914 D-loop; other site 1427342004915 H-loop/switch region; other site 1427342004916 NAD(P)H-dependent FMN reductase; Provisional; Region: PRK10569 1427342004917 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342004918 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342004919 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342004920 substrate binding pocket [chemical binding]; other site 1427342004921 membrane-bound complex binding site; other site 1427342004922 hinge residues; other site 1427342004923 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 1427342004924 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 1427342004925 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342004926 active site 1427342004927 dimer interface [polypeptide binding]; other site 1427342004928 non-prolyl cis peptide bond; other site 1427342004929 insertion regions; other site 1427342004930 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342004931 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342004932 dimer interface [polypeptide binding]; other site 1427342004933 conserved gate region; other site 1427342004934 putative PBP binding loops; other site 1427342004935 ABC-ATPase subunit interface; other site 1427342004936 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 1427342004937 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342004938 Walker A/P-loop; other site 1427342004939 ATP binding site [chemical binding]; other site 1427342004940 Q-loop/lid; other site 1427342004941 ABC transporter signature motif; other site 1427342004942 Walker B; other site 1427342004943 D-loop; other site 1427342004944 H-loop/switch region; other site 1427342004945 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 1427342004946 HopJ type III effector protein; Region: HopJ; pfam08888 1427342004947 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3492 1427342004948 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 1427342004949 homooctamer interface [polypeptide binding]; other site 1427342004950 active site 1427342004951 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 1427342004952 homodecamer interface [polypeptide binding]; other site 1427342004953 GTP cyclohydrolase I; Provisional; Region: PLN03044 1427342004954 active site 1427342004955 putative catalytic site residues [active] 1427342004956 zinc binding site [ion binding]; other site 1427342004957 GTP-CH-I/GFRP interaction surface; other site 1427342004958 dihydromonapterin reductase; Provisional; Region: PRK06483 1427342004959 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342004960 NAD(P) binding site [chemical binding]; other site 1427342004961 active site 1427342004962 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 1427342004963 flavodoxin; Provisional; Region: PRK05723 1427342004964 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342004965 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342004966 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 1427342004967 putative dimerization interface [polypeptide binding]; other site 1427342004968 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 1427342004969 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 1427342004970 aldolase II superfamily protein; Provisional; Region: PRK07044 1427342004971 intersubunit interface [polypeptide binding]; other site 1427342004972 active site 1427342004973 Zn2+ binding site [ion binding]; other site 1427342004974 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342004975 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 1427342004976 homodimer interface [polypeptide binding]; other site 1427342004977 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 1427342004978 NAD binding site [chemical binding]; other site 1427342004979 active site 1427342004980 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 1427342004981 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342004982 substrate binding site [chemical binding]; other site 1427342004983 oxyanion hole (OAH) forming residues; other site 1427342004984 trimer interface [polypeptide binding]; other site 1427342004985 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 1427342004986 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342004987 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342004988 SnoaL-like domain; Region: SnoaL_2; pfam12680 1427342004989 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342004990 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342004991 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 1427342004992 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 1427342004993 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 1427342004994 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342004995 DNA binding residues [nucleotide binding] 1427342004996 dimerization interface [polypeptide binding]; other site 1427342004997 Uncharacterized conserved protein [Function unknown]; Region: COG2912 1427342004998 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 1427342004999 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 1427342005000 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1427342005001 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 1427342005002 NAD binding site [chemical binding]; other site 1427342005003 Phe binding site; other site 1427342005004 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 1427342005005 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 1427342005006 TPP-binding site [chemical binding]; other site 1427342005007 tetramer interface [polypeptide binding]; other site 1427342005008 heterodimer interface [polypeptide binding]; other site 1427342005009 phosphorylation loop region [posttranslational modification] 1427342005010 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 1427342005011 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 1427342005012 alpha subunit interface [polypeptide binding]; other site 1427342005013 TPP binding site [chemical binding]; other site 1427342005014 heterodimer interface [polypeptide binding]; other site 1427342005015 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1427342005016 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 1427342005017 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342005018 E3 interaction surface; other site 1427342005019 lipoyl attachment site [posttranslational modification]; other site 1427342005020 e3 binding domain; Region: E3_binding; pfam02817 1427342005021 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1427342005022 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 1427342005023 DNA damage-inducible gene in SOS regulon, dependent on cyclic AMP and H-NS , pqiA [General function prediction only]; Region: COG3141 1427342005024 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342005025 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 1427342005026 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342005027 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342005028 DNA binding residues [nucleotide binding] 1427342005029 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342005030 FecR protein; Region: FecR; pfam04773 1427342005031 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342005032 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 1427342005033 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342005034 N-terminal plug; other site 1427342005035 ligand-binding site [chemical binding]; other site 1427342005036 Heme-binding protein A (HasA); Region: HasA; pfam06438 1427342005037 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 1427342005038 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1427342005039 Walker A/P-loop; other site 1427342005040 ATP binding site [chemical binding]; other site 1427342005041 Q-loop/lid; other site 1427342005042 ABC transporter signature motif; other site 1427342005043 Walker B; other site 1427342005044 D-loop; other site 1427342005045 H-loop/switch region; other site 1427342005046 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1427342005047 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342005048 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342005049 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 1427342005050 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 1427342005051 Predicted membrane protein [Function unknown]; Region: COG3223 1427342005052 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342005053 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342005054 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1427342005055 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1427342005056 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 1427342005057 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1427342005058 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1427342005059 Protein of unknown function (DUF1375); Region: DUF1375; pfam07119 1427342005060 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 1427342005061 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005062 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 1427342005063 putative dimerization interface [polypeptide binding]; other site 1427342005064 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 1427342005065 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 1427342005066 FAD binding pocket [chemical binding]; other site 1427342005067 FAD binding motif [chemical binding]; other site 1427342005068 phosphate binding motif [ion binding]; other site 1427342005069 beta-alpha-beta structure motif; other site 1427342005070 NAD binding pocket [chemical binding]; other site 1427342005071 NosL; Region: NosL; cl01769 1427342005072 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 1427342005073 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1427342005074 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1427342005075 Walker A/P-loop; other site 1427342005076 ATP binding site [chemical binding]; other site 1427342005077 Q-loop/lid; other site 1427342005078 ABC transporter signature motif; other site 1427342005079 Walker B; other site 1427342005080 D-loop; other site 1427342005081 H-loop/switch region; other site 1427342005082 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 1427342005083 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 1427342005084 nitrous-oxide reductase; Validated; Region: PRK02888 1427342005085 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1427342005086 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 1427342005087 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 1427342005088 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1427342005089 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 1427342005090 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342005091 active site 1427342005092 metal binding site [ion binding]; metal-binding site 1427342005093 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342005094 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 1427342005095 homodimer interaction site [polypeptide binding]; other site 1427342005096 cofactor binding site; other site 1427342005097 RhlG and related beta-ketoacyl reductases, classical (c) SDRs; Region: RhlG_SDR_c; cd08942 1427342005098 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 1427342005099 NADP binding site [chemical binding]; other site 1427342005100 active site 1427342005101 Protein of Unknown function (DUF2784); Region: DUF2784; pfam10861 1427342005102 Arc-like DNA binding domain; Region: Arc; pfam03869 1427342005103 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 1427342005104 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 1427342005105 Walker A/P-loop; other site 1427342005106 ATP binding site [chemical binding]; other site 1427342005107 Q-loop/lid; other site 1427342005108 ABC transporter signature motif; other site 1427342005109 Walker B; other site 1427342005110 D-loop; other site 1427342005111 H-loop/switch region; other site 1427342005112 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 1427342005113 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 1427342005114 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342005115 dimer interface [polypeptide binding]; other site 1427342005116 conserved gate region; other site 1427342005117 ABC-ATPase subunit interface; other site 1427342005118 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 1427342005119 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342005120 DNA-binding site [nucleotide binding]; DNA binding site 1427342005121 UTRA domain; Region: UTRA; pfam07702 1427342005122 Phosphonate metabolism protein PhnG; Region: PhnG; pfam06754 1427342005123 Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnH; COG3625 1427342005124 Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnI; COG3626 1427342005125 Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnJ; COG3627 1427342005126 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 1427342005127 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342005128 Walker A/P-loop; other site 1427342005129 ATP binding site [chemical binding]; other site 1427342005130 Q-loop/lid; other site 1427342005131 ABC transporter signature motif; other site 1427342005132 Walker B; other site 1427342005133 D-loop; other site 1427342005134 H-loop/switch region; other site 1427342005135 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342005136 ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PhnL; COG4778 1427342005137 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342005138 Walker A/P-loop; other site 1427342005139 ATP binding site [chemical binding]; other site 1427342005140 Q-loop/lid; other site 1427342005141 ABC transporter signature motif; other site 1427342005142 Walker B; other site 1427342005143 D-loop; other site 1427342005144 H-loop/switch region; other site 1427342005145 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: COG3454 1427342005146 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 1427342005147 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 1427342005148 active site 1427342005149 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 1427342005150 AAA domain; Region: AAA_18; pfam13238 1427342005151 active site 1427342005152 carbon-phosphorus lyase complex accessory protein; Provisional; Region: phnP; PRK11244 1427342005153 putative hydrolase; Provisional; Region: PRK02113 1427342005154 Histone acetyltransferase HPA2 and related acetyltransferases [Transcription / General function prediction only]; Region: WecD; COG0454 1427342005155 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342005156 Coenzyme A binding pocket [chemical binding]; other site 1427342005157 hypothetical protein; Provisional; Region: PRK10040 1427342005158 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 1427342005159 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 1427342005160 multimer interface [polypeptide binding]; other site 1427342005161 active site 1427342005162 catalytic triad [active] 1427342005163 dimer interface [polypeptide binding]; other site 1427342005164 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 1427342005165 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342005166 Walker A motif; other site 1427342005167 ATP binding site [chemical binding]; other site 1427342005168 Walker B motif; other site 1427342005169 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1427342005170 Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family; Region: PBP1_AmiC; cd06357 1427342005171 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 1427342005172 ligand binding site [chemical binding]; other site 1427342005173 regulator interaction site; other site 1427342005174 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 1427342005175 ANTAR domain; Region: ANTAR; pfam03861 1427342005176 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 1427342005177 Fucose-binding lectin II (PA-IIL); Region: PA-IIL; pfam07472 1427342005178 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1427342005179 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342005180 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342005181 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 1427342005182 EamA-like transporter family; Region: EamA; cl17759 1427342005183 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 1427342005184 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 1427342005185 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342005186 catalytic residue [active] 1427342005187 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342005188 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342005189 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342005190 putative substrate translocation pore; other site 1427342005191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3222 1427342005192 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 1427342005193 Flagellar regulator YcgR; Region: YcgR; pfam07317 1427342005194 PilZ domain; Region: PilZ; pfam07238 1427342005195 Flagellar biosynthesis/type III secretory pathway chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3418 1427342005196 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 1427342005197 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 1427342005198 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 1427342005199 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 1427342005200 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1427342005201 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342005202 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342005203 active site 1427342005204 phosphorylation site [posttranslational modification] 1427342005205 intermolecular recognition site; other site 1427342005206 dimerization interface [polypeptide binding]; other site 1427342005207 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 1427342005208 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 1427342005209 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342005210 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 1427342005211 anti sigma factor interaction site; other site 1427342005212 regulatory phosphorylation site [posttranslational modification]; other site 1427342005213 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342005214 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342005215 active site 1427342005216 phosphorylation site [posttranslational modification] 1427342005217 intermolecular recognition site; other site 1427342005218 dimerization interface [polypeptide binding]; other site 1427342005219 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 1427342005220 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 1427342005221 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 1427342005222 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342005223 putative binding surface; other site 1427342005224 active site 1427342005225 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 1427342005226 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342005227 ATP binding site [chemical binding]; other site 1427342005228 putative Mg++ binding site [ion binding]; other site 1427342005229 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342005230 nucleotide binding region [chemical binding]; other site 1427342005231 ATP-binding site [chemical binding]; other site 1427342005232 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 1427342005233 HRDC domain; Region: HRDC; pfam00570 1427342005234 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342005235 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342005236 metal binding site [ion binding]; metal-binding site 1427342005237 active site 1427342005238 I-site; other site 1427342005239 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 1427342005240 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 1427342005241 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342005242 MarR family; Region: MarR_2; pfam12802 1427342005243 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 1427342005244 FimV N-terminal domain; Region: FimV_core; TIGR03505 1427342005245 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 1427342005246 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 1427342005247 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 1427342005248 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 1427342005249 active site 1427342005250 nucleophile elbow; other site 1427342005251 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1427342005252 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 1427342005253 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342005254 Surface antigen; Region: Bac_surface_Ag; pfam01103 1427342005255 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]; Region: COG3526 1427342005256 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 1427342005257 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 1427342005258 NADP binding site [chemical binding]; other site 1427342005259 homopentamer interface [polypeptide binding]; other site 1427342005260 substrate binding site [chemical binding]; other site 1427342005261 active site 1427342005262 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342005263 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342005264 putative substrate translocation pore; other site 1427342005265 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342005266 S-adenosylmethionine binding site [chemical binding]; other site 1427342005267 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1427342005268 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 1427342005269 dimer interface [polypeptide binding]; other site 1427342005270 active site 1427342005271 CoA binding pocket [chemical binding]; other site 1427342005272 Ketosteroid isomerase-related protein [General function prediction only]; Region: COG3631 1427342005273 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 1427342005274 Cytochrome P450; Region: p450; cl12078 1427342005275 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342005276 short chain dehydrogenase; Provisional; Region: PRK06914 1427342005277 NAD(P) binding site [chemical binding]; other site 1427342005278 active site 1427342005279 Condensation domain; Region: Condensation; pfam00668 1427342005280 Wax ester synthase-like Acyl-CoA acyltransferase domain; Region: WES_acyltransf; pfam03007 1427342005281 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 1427342005282 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342005283 Condensation domain; Region: Condensation; pfam00668 1427342005284 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342005285 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342005286 acyl-activating enzyme (AAE) consensus motif; other site 1427342005287 AMP binding site [chemical binding]; other site 1427342005288 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342005289 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 1427342005290 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342005291 acyl-activating enzyme (AAE) consensus motif; other site 1427342005292 AMP binding site [chemical binding]; other site 1427342005293 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342005294 ATP-dependent Clp protease proteolytic subunit; Reviewed; Region: PRK12553 1427342005295 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1427342005296 oligomer interface [polypeptide binding]; other site 1427342005297 active site residues [active] 1427342005298 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 1427342005299 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 1427342005300 short chain dehydrogenase; Validated; Region: PRK05855 1427342005301 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342005302 classical (c) SDRs; Region: SDR_c; cd05233 1427342005303 NAD(P) binding site [chemical binding]; other site 1427342005304 active site 1427342005305 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 1427342005306 active site 1427342005307 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg2; cd04778 1427342005308 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1427342005309 DNA binding residues [nucleotide binding] 1427342005310 putative dimer interface [polypeptide binding]; other site 1427342005311 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342005312 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005313 The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; Region: PBP2_ToxR; cd08465 1427342005314 putative substrate binding pocket [chemical binding]; other site 1427342005315 putative dimerization interface [polypeptide binding]; other site 1427342005316 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3238 1427342005317 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 1427342005318 Phosphoesterase family; Region: Phosphoesterase; pfam04185 1427342005319 Domain of unknown function (DUF756); Region: DUF756; pfam05506 1427342005320 Domain of unknown function (DUF756); Region: DUF756; pfam05506 1427342005321 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 1427342005322 ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism]; Region: COG3639 1427342005323 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 1427342005324 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 1427342005325 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342005326 Walker A/P-loop; other site 1427342005327 ATP binding site [chemical binding]; other site 1427342005328 Q-loop/lid; other site 1427342005329 ABC transporter signature motif; other site 1427342005330 Walker B; other site 1427342005331 D-loop; other site 1427342005332 H-loop/switch region; other site 1427342005333 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 1427342005334 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342005335 substrate binding pocket [chemical binding]; other site 1427342005336 membrane-bound complex binding site; other site 1427342005337 hinge residues; other site 1427342005338 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 1427342005339 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1427342005340 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 1427342005341 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 1427342005342 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 1427342005343 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342005344 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342005345 metal binding site [ion binding]; metal-binding site 1427342005346 active site 1427342005347 I-site; other site 1427342005348 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342005349 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1427342005350 Sulfatase; Region: Sulfatase; pfam00884 1427342005351 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342005352 Ligand Binding Site [chemical binding]; other site 1427342005353 ATP-dependent helicase HepA; Validated; Region: PRK04914 1427342005354 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342005355 ATP binding site [chemical binding]; other site 1427342005356 putative Mg++ binding site [ion binding]; other site 1427342005357 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342005358 nucleotide binding region [chemical binding]; other site 1427342005359 ATP-binding site [chemical binding]; other site 1427342005360 Alkylated DNA repair protein [DNA replication, recombination, and repair]; Region: AlkB; COG3145 1427342005361 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342005362 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342005363 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 1427342005364 HlyD family secretion protein; Region: HlyD; pfam00529 1427342005365 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342005366 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342005367 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342005368 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 1427342005369 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 1427342005370 dimer interaction site [polypeptide binding]; other site 1427342005371 substrate-binding tunnel; other site 1427342005372 active site 1427342005373 catalytic site [active] 1427342005374 substrate binding site [chemical binding]; other site 1427342005375 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1427342005376 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342005377 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342005378 long-chain-fatty-acid--CoA ligase; Provisional; Region: PRK12492 1427342005379 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 1427342005380 acyl-activating enzyme (AAE) consensus motif; other site 1427342005381 putative AMP binding site [chemical binding]; other site 1427342005382 putative active site [active] 1427342005383 putative CoA binding site [chemical binding]; other site 1427342005384 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 1427342005385 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 1427342005386 acyl-activating enzyme (AAE) consensus motif; other site 1427342005387 putative AMP binding site [chemical binding]; other site 1427342005388 putative active site [active] 1427342005389 putative CoA binding site [chemical binding]; other site 1427342005390 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 1427342005391 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342005392 ATP binding site [chemical binding]; other site 1427342005393 putative Mg++ binding site [ion binding]; other site 1427342005394 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342005395 nucleotide binding region [chemical binding]; other site 1427342005396 ATP-binding site [chemical binding]; other site 1427342005397 Helicase associated domain (HA2); Region: HA2; pfam04408 1427342005398 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 1427342005399 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 1427342005400 alkaline phosphatase; Provisional; Region: PRK10518 1427342005401 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 1427342005402 active site 1427342005403 dimer interface [polypeptide binding]; other site 1427342005404 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 1427342005405 HIT family signature motif; other site 1427342005406 catalytic residue [active] 1427342005407 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342005408 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342005409 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342005410 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 1427342005411 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 1427342005412 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 1427342005413 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 1427342005414 Amidases related to nicotinamidase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PncA; COG1335 1427342005415 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342005416 catalytic triad [active] 1427342005417 conserved cis-peptide bond; other site 1427342005418 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1427342005419 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1427342005420 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1427342005421 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 1427342005422 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 1427342005423 dimer interface [polypeptide binding]; other site 1427342005424 active site 1427342005425 CoA binding pocket [chemical binding]; other site 1427342005426 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1427342005427 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342005428 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342005429 DNA binding residues [nucleotide binding] 1427342005430 Putative zinc-finger; Region: zf-HC2; pfam13490 1427342005431 Uncharacterized low-complexity protein [Function unknown]; Region: COG3767 1427342005432 Protein of unknown function (DUF692); Region: DUF692; pfam05114 1427342005433 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3219 1427342005434 Predicted membrane protein [Function unknown]; Region: COG2259 1427342005435 Phosphate-selective porin [Inorganic ion transport and metabolism]; Region: OprP; COG3746 1427342005436 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 1427342005437 Phosphate-selective porin [Inorganic ion transport and metabolism]; Region: OprP; COG3746 1427342005438 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 1427342005439 short chain dehydrogenase; Provisional; Region: PRK05650 1427342005440 classical (c) SDRs; Region: SDR_c; cd05233 1427342005441 NAD(P) binding site [chemical binding]; other site 1427342005442 active site 1427342005443 Uncharacterized conserved protein [Function unknown]; Region: COG1742 1427342005444 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 1427342005445 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342005446 ATP binding site [chemical binding]; other site 1427342005447 putative Mg++ binding site [ion binding]; other site 1427342005448 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342005449 nucleotide binding region [chemical binding]; other site 1427342005450 ATP-binding site [chemical binding]; other site 1427342005451 DEAD/H associated; Region: DEAD_assoc; pfam08494 1427342005452 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 1427342005453 Na binding site [ion binding]; other site 1427342005454 PAS fold; Region: PAS_7; pfam12860 1427342005455 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342005456 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342005457 dimer interface [polypeptide binding]; other site 1427342005458 phosphorylation site [posttranslational modification] 1427342005459 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342005460 ATP binding site [chemical binding]; other site 1427342005461 Mg2+ binding site [ion binding]; other site 1427342005462 G-X-G motif; other site 1427342005463 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342005464 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342005465 active site 1427342005466 phosphorylation site [posttranslational modification] 1427342005467 intermolecular recognition site; other site 1427342005468 dimerization interface [polypeptide binding]; other site 1427342005469 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1427342005470 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1427342005471 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342005472 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342005473 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342005474 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342005475 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1427342005476 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342005477 N-terminal plug; other site 1427342005478 ligand-binding site [chemical binding]; other site 1427342005479 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342005480 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342005481 putative substrate translocation pore; other site 1427342005482 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342005483 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1427342005484 putative acyl-acceptor binding pocket; other site 1427342005485 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342005486 DNA-binding site [nucleotide binding]; DNA binding site 1427342005487 RNA-binding motif; other site 1427342005488 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 1427342005489 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 1427342005490 Sodium Bile acid symporter family; Region: SBF; pfam01758 1427342005491 recombination associated protein; Reviewed; Region: rdgC; PRK00321 1427342005492 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 1427342005493 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 1427342005494 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342005495 Uncharacterized conserved protein [Function unknown]; Region: COG3339 1427342005496 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342005497 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342005498 substrate binding pocket [chemical binding]; other site 1427342005499 membrane-bound complex binding site; other site 1427342005500 hinge residues; other site 1427342005501 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342005502 non-specific DNA binding site [nucleotide binding]; other site 1427342005503 salt bridge; other site 1427342005504 sequence-specific DNA binding site [nucleotide binding]; other site 1427342005505 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342005506 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 1427342005507 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342005508 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342005509 metal binding site [ion binding]; metal-binding site 1427342005510 active site 1427342005511 I-site; other site 1427342005512 carboxy-terminal protease; Provisional; Region: PRK11186 1427342005513 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1427342005514 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 1427342005515 protein binding site [polypeptide binding]; other site 1427342005516 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1427342005517 Catalytic dyad [active] 1427342005518 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 1427342005519 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 1427342005520 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 1427342005521 NAD(P) binding site [chemical binding]; other site 1427342005522 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 1427342005523 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342005524 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1427342005525 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342005526 Walker A/P-loop; other site 1427342005527 ATP binding site [chemical binding]; other site 1427342005528 Q-loop/lid; other site 1427342005529 ABC transporter signature motif; other site 1427342005530 Walker B; other site 1427342005531 D-loop; other site 1427342005532 H-loop/switch region; other site 1427342005533 TOBE domain; Region: TOBE_2; pfam08402 1427342005534 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342005535 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342005536 dimer interface [polypeptide binding]; other site 1427342005537 conserved gate region; other site 1427342005538 putative PBP binding loops; other site 1427342005539 ABC-ATPase subunit interface; other site 1427342005540 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1427342005541 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342005542 dimer interface [polypeptide binding]; other site 1427342005543 conserved gate region; other site 1427342005544 putative PBP binding loops; other site 1427342005545 ABC-ATPase subunit interface; other site 1427342005546 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 1427342005547 Phosphopentomutase [Carbohydrate transport and metabolism]; Region: DeoB; cl17415 1427342005548 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342005549 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1427342005550 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342005551 DNA-binding site [nucleotide binding]; DNA binding site 1427342005552 transcriptional regulator protein; Region: phnR; TIGR03337 1427342005553 UTRA domain; Region: UTRA; pfam07702 1427342005554 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1427342005555 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1427342005556 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 1427342005557 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 1427342005558 active site 1427342005559 metal binding site [ion binding]; metal-binding site 1427342005560 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1427342005561 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1427342005562 active site 1427342005563 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 1427342005564 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 1427342005565 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 1427342005566 Switch I; other site 1427342005567 Switch II; other site 1427342005568 septum formation inhibitor; Reviewed; Region: minC; PRK00339 1427342005569 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 1427342005570 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 1427342005571 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1427342005572 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1427342005573 putative acyl-acceptor binding pocket; other site 1427342005574 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 1427342005575 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 1427342005576 active site 1427342005577 nucleophile elbow; other site 1427342005578 Pirin-related protein [General function prediction only]; Region: COG1741 1427342005579 Pirin; Region: Pirin; pfam02678 1427342005580 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1427342005581 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1427342005582 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342005583 Predicted membrane protein [Function unknown]; Region: COG3205 1427342005584 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342005585 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 1427342005586 Predicted membrane protein [Function unknown]; Region: COG3162 1427342005587 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1427342005588 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 1427342005589 Na binding site [ion binding]; other site 1427342005590 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 1427342005591 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342005592 ligand binding site [chemical binding]; other site 1427342005593 flexible hinge region; other site 1427342005594 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP...; Region: CBS_pair_CAP-ED_DUF294_assoc_bac; cd04589 1427342005595 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 1427342005596 metal binding triad; other site 1427342005597 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 1427342005598 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1427342005599 active site 1427342005600 catalytic site [active] 1427342005601 substrate binding site [chemical binding]; other site 1427342005602 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 1427342005603 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 1427342005604 Protein of unknown function, DUF482; Region: DUF482; pfam04339 1427342005605 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342005606 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1427342005607 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342005608 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 1427342005609 Walker A/P-loop; other site 1427342005610 ATP binding site [chemical binding]; other site 1427342005611 Q-loop/lid; other site 1427342005612 ABC transporter signature motif; other site 1427342005613 Walker B; other site 1427342005614 D-loop; other site 1427342005615 H-loop/switch region; other site 1427342005616 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 1427342005617 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 1427342005618 substrate binding site [chemical binding]; other site 1427342005619 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342005620 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 1427342005621 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1427342005622 catalytic site [active] 1427342005623 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342005624 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005625 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342005626 dimerization interface [polypeptide binding]; other site 1427342005627 Acyl carrier protein phosphodiesterase [Lipid metabolism]; Region: AcpD; COG1182 1427342005628 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342005629 EamA-like transporter family; Region: EamA; pfam00892 1427342005630 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 1427342005631 dimer interface [polypeptide binding]; other site 1427342005632 putative tRNA-binding site [nucleotide binding]; other site 1427342005633 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342005634 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342005635 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342005636 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1427342005637 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1427342005638 putative active site [active] 1427342005639 putative metal binding site [ion binding]; other site 1427342005640 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342005641 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 1427342005642 MASE2 domain; Region: MASE2; pfam05230 1427342005643 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 1427342005644 cyclase homology domain; Region: CHD; cd07302 1427342005645 nucleotidyl binding site; other site 1427342005646 metal binding site [ion binding]; metal-binding site 1427342005647 dimer interface [polypeptide binding]; other site 1427342005648 Predicted membrane protein [Function unknown]; Region: COG4323 1427342005649 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342005650 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342005651 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342005652 ABC-type uncharacterized transport system, auxiliary component [General function prediction only]; Region: COG3218 1427342005653 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1427342005654 mce related protein; Region: MCE; pfam02470 1427342005655 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1427342005656 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342005657 Walker A/P-loop; other site 1427342005658 ATP binding site [chemical binding]; other site 1427342005659 Q-loop/lid; other site 1427342005660 ABC transporter signature motif; other site 1427342005661 Walker B; other site 1427342005662 D-loop; other site 1427342005663 H-loop/switch region; other site 1427342005664 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1427342005665 Permease; Region: Permease; pfam02405 1427342005666 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 1427342005667 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 1427342005668 Flagellin N-methylase; Region: FliB; cl00497 1427342005669 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 1427342005670 putative FMN binding site [chemical binding]; other site 1427342005671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342005672 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342005673 dimerization interface [polypeptide binding]; other site 1427342005674 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342005675 ATP binding site [chemical binding]; other site 1427342005676 Mg2+ binding site [ion binding]; other site 1427342005677 G-X-G motif; other site 1427342005678 P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]; Region: CpxP; COG3678 1427342005679 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342005680 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342005681 active site 1427342005682 phosphorylation site [posttranslational modification] 1427342005683 intermolecular recognition site; other site 1427342005684 dimerization interface [polypeptide binding]; other site 1427342005685 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342005686 DNA binding site [nucleotide binding] 1427342005687 YciI-like protein; Reviewed; Region: PRK11370 1427342005688 intracellular septation protein A; Reviewed; Region: PRK00259 1427342005689 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 1427342005690 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 1427342005691 active site 1427342005692 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 1427342005693 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1427342005694 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 1427342005695 Chromosome segregation and condensation protein B [DNA replication, recombination and repair]; Region: scpB; COG1386 1427342005696 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 1427342005697 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 1427342005698 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 1427342005699 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1427342005700 phosphogluconate dehydratase; Validated; Region: PRK09054 1427342005701 6-phosphogluconate dehydratase; Region: edd; TIGR01196 1427342005702 glucokinase, proteobacterial type; Region: glk; TIGR00749 1427342005703 glucokinase; Provisional; Region: glk; PRK00292 1427342005704 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342005705 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342005706 active site 1427342005707 phosphorylation site [posttranslational modification] 1427342005708 intermolecular recognition site; other site 1427342005709 dimerization interface [polypeptide binding]; other site 1427342005710 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342005711 DNA binding site [nucleotide binding] 1427342005712 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 1427342005713 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342005714 ATP binding site [chemical binding]; other site 1427342005715 Mg2+ binding site [ion binding]; other site 1427342005716 G-X-G motif; other site 1427342005717 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 1427342005718 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 1427342005719 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342005720 dimer interface [polypeptide binding]; other site 1427342005721 conserved gate region; other site 1427342005722 putative PBP binding loops; other site 1427342005723 ABC-ATPase subunit interface; other site 1427342005724 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 1427342005725 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342005726 dimer interface [polypeptide binding]; other site 1427342005727 conserved gate region; other site 1427342005728 putative PBP binding loops; other site 1427342005729 ABC-ATPase subunit interface; other site 1427342005730 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 1427342005731 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 1427342005732 Walker A/P-loop; other site 1427342005733 ATP binding site [chemical binding]; other site 1427342005734 Q-loop/lid; other site 1427342005735 ABC transporter signature motif; other site 1427342005736 Walker B; other site 1427342005737 D-loop; other site 1427342005738 H-loop/switch region; other site 1427342005739 TOBE domain; Region: TOBE; pfam03459 1427342005740 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 1427342005741 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 1427342005742 active site 1427342005743 phosphate binding residues; other site 1427342005744 catalytic residues [active] 1427342005745 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 1427342005746 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 1427342005747 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 1427342005748 putative active site [active] 1427342005749 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 1427342005750 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1427342005751 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1427342005752 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 1427342005753 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 1427342005754 putative active site [active] 1427342005755 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 1427342005756 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 1427342005757 active site 1427342005758 intersubunit interface [polypeptide binding]; other site 1427342005759 catalytic residue [active] 1427342005760 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_23; cd04682 1427342005761 nudix motif; other site 1427342005762 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 1427342005763 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342005764 RNA binding surface [nucleotide binding]; other site 1427342005765 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 1427342005766 probable active site [active] 1427342005767 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342005768 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342005769 metal binding site [ion binding]; metal-binding site 1427342005770 active site 1427342005771 I-site; other site 1427342005772 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 1427342005773 agmatinase; Region: agmatinase; TIGR01230 1427342005774 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 1427342005775 putative active site [active] 1427342005776 putative metal binding site [ion binding]; other site 1427342005777 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342005778 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 1427342005779 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342005780 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 1427342005781 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342005782 NAD(P) binding site [chemical binding]; other site 1427342005783 active site 1427342005784 phosphoglycolate phosphatase; Provisional; Region: PRK13222 1427342005785 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342005786 motif II; other site 1427342005787 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1427342005788 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342005789 S-adenosylmethionine binding site [chemical binding]; other site 1427342005790 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 1427342005791 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 1427342005792 active site 1427342005793 putative substrate binding pocket [chemical binding]; other site 1427342005794 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 1427342005795 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182 1427342005796 DNA gyrase subunit A; Validated; Region: PRK05560 1427342005797 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 1427342005798 CAP-like domain; other site 1427342005799 active site 1427342005800 primary dimer interface [polypeptide binding]; other site 1427342005801 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005802 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005803 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005804 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005805 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005806 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1427342005807 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 1427342005808 homodimer interface [polypeptide binding]; other site 1427342005809 substrate-cofactor binding pocket; other site 1427342005810 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342005811 catalytic residue [active] 1427342005812 Chorismate mutase type II; Region: CM_2; cl00693 1427342005813 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 1427342005814 Prephenate dehydratase; Region: PDT; pfam00800 1427342005815 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 1427342005816 putative L-Phe binding site [chemical binding]; other site 1427342005817 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 1427342005818 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342005819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342005820 homodimer interface [polypeptide binding]; other site 1427342005821 catalytic residue [active] 1427342005822 bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK14806 1427342005823 prephenate dehydrogenase; Validated; Region: PRK08507 1427342005824 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 1427342005825 hinge; other site 1427342005826 active site 1427342005827 cytidylate kinase; Provisional; Region: cmk; PRK00023 1427342005828 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 1427342005829 CMP-binding site; other site 1427342005830 The sites determining sugar specificity; other site 1427342005831 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1427342005832 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 1427342005833 RNA binding site [nucleotide binding]; other site 1427342005834 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 1427342005835 RNA binding site [nucleotide binding]; other site 1427342005836 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 1427342005837 RNA binding site [nucleotide binding]; other site 1427342005838 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1427342005839 RNA binding site [nucleotide binding]; other site 1427342005840 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1427342005841 RNA binding site [nucleotide binding]; other site 1427342005842 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 1427342005843 RNA binding site [nucleotide binding]; other site 1427342005844 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 1427342005845 IHF dimer interface [polypeptide binding]; other site 1427342005846 IHF - DNA interface [nucleotide binding]; other site 1427342005847 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 1427342005848 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342005849 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members; Region: 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_; cd08255 1427342005850 putative NAD(P) binding site [chemical binding]; other site 1427342005851 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1427342005852 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1427342005853 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1427342005854 Heparinase II/III-like protein; Region: Hepar_II_III; pfam07940 1427342005855 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342005856 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 1427342005857 Bacterial sugar transferase; Region: Bac_transf; cl00939 1427342005858 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1427342005859 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 1427342005860 inhibitor-cofactor binding pocket; inhibition site 1427342005861 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342005862 catalytic residue [active] 1427342005863 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1427342005864 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 1427342005865 Mg++ binding site [ion binding]; other site 1427342005866 putative catalytic motif [active] 1427342005867 putative substrate binding site [chemical binding]; other site 1427342005868 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 1427342005869 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1427342005870 NAD(P) binding site [chemical binding]; other site 1427342005871 homodimer interface [polypeptide binding]; other site 1427342005872 substrate binding site [chemical binding]; other site 1427342005873 active site 1427342005874 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 1427342005875 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 1427342005876 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342005877 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342005878 homodimer interface [polypeptide binding]; other site 1427342005879 catalytic residue [active] 1427342005880 excinuclease ABC subunit B; Provisional; Region: PRK05298 1427342005881 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342005882 ATP binding site [chemical binding]; other site 1427342005883 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342005884 nucleotide binding region [chemical binding]; other site 1427342005885 ATP-binding site [chemical binding]; other site 1427342005886 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1427342005887 UvrB/uvrC motif; Region: UVR; pfam02151 1427342005888 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342005889 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342005890 putative substrate translocation pore; other site 1427342005891 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1427342005892 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342005893 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342005894 LysR family transcriptional regulator; Provisional; Region: PRK14997 1427342005895 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005896 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342005897 putative effector binding pocket; other site 1427342005898 dimerization interface [polypeptide binding]; other site 1427342005899 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 1427342005900 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1427342005901 HIGH motif; other site 1427342005902 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1427342005903 active site 1427342005904 KMSKS motif; other site 1427342005905 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342005906 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342005907 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 1427342005908 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342005909 Entner-Doudoroff aldolase; Region: eda; TIGR01182 1427342005910 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 1427342005911 active site 1427342005912 intersubunit interface [polypeptide binding]; other site 1427342005913 catalytic residue [active] 1427342005914 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342005915 active site 1427342005916 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 1427342005917 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 1427342005918 FMN binding site [chemical binding]; other site 1427342005919 active site 1427342005920 catalytic residues [active] 1427342005921 substrate binding site [chemical binding]; other site 1427342005922 short chain dehydrogenase; Provisional; Region: PRK06123 1427342005923 classical (c) SDRs; Region: SDR_c; cd05233 1427342005924 NAD(P) binding site [chemical binding]; other site 1427342005925 active site 1427342005926 BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins; Region: BLMT_like; cd08350 1427342005927 dimer interface [polypeptide binding]; other site 1427342005928 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342005929 ligand binding site [chemical binding]; other site 1427342005930 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342005931 Coenzyme A binding pocket [chemical binding]; other site 1427342005932 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1427342005933 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 1427342005934 putative dimer interface [polypeptide binding]; other site 1427342005935 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 1427342005936 active site 1427342005937 catalytic triad [active] 1427342005938 oxyanion hole [active] 1427342005939 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342005940 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005941 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342005942 dimerization interface [polypeptide binding]; other site 1427342005943 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 1427342005944 homotrimer interaction site [polypeptide binding]; other site 1427342005945 putative active site [active] 1427342005946 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342005947 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342005948 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342005949 dimerization interface [polypeptide binding]; other site 1427342005950 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 1427342005951 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 1427342005952 substrate binding site [chemical binding]; other site 1427342005953 ligand binding site [chemical binding]; other site 1427342005954 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 1427342005955 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 1427342005956 substrate binding site [chemical binding]; other site 1427342005957 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342005958 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342005959 S-adenosylmethionine binding site [chemical binding]; other site 1427342005960 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 1427342005961 tartrate dehydrogenase; Region: TTC; TIGR02089 1427342005962 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 1427342005963 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1427342005964 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK05671 1427342005965 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1427342005966 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 1427342005967 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342005968 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 1427342005969 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1427342005970 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1427342005971 dimerization interface 3.5A [polypeptide binding]; other site 1427342005972 active site 1427342005973 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 1427342005974 active site 1427342005975 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 1427342005976 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1427342005977 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1427342005978 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342005979 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 1427342005980 Sporulation related domain; Region: SPOR; pfam05036 1427342005981 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1427342005982 Colicin V production protein; Region: Colicin_V; pfam02674 1427342005983 amidophosphoribosyltransferase; Provisional; Region: PRK09246 1427342005984 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 1427342005985 active site 1427342005986 tetramer interface [polypeptide binding]; other site 1427342005987 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342005988 active site 1427342005989 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 1427342005990 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 1427342005991 homodimer interface [polypeptide binding]; other site 1427342005992 substrate-cofactor binding pocket; other site 1427342005993 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342005994 catalytic residue [active] 1427342005995 oxidoreductase; Validated; Region: PRK05717 1427342005996 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342005997 NAD(P) binding site [chemical binding]; other site 1427342005998 active site 1427342005999 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 1427342006000 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342006001 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342006002 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342006003 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342006004 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 1427342006005 type II secretion system protein E; Region: type_II_gspE; TIGR02533 1427342006006 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 1427342006007 Walker A motif; other site 1427342006008 ATP binding site [chemical binding]; other site 1427342006009 Walker B motif; other site 1427342006010 type II secretion system protein F; Region: GspF; TIGR02120 1427342006011 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342006012 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342006013 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 1427342006014 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 1427342006015 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1427342006016 type II secretion system protein I; Region: gspI; TIGR01707 1427342006017 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 1427342006018 type II secretion system protein J; Region: gspJ; TIGR01711 1427342006019 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 1427342006020 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 1427342006021 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 1427342006022 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 1427342006023 GspL periplasmic domain; Region: GspL_C; pfam12693 1427342006024 Type II secretory pathway, component PulM [Intracellular trafficking and secretion]; Region: PulM; COG3149 1427342006025 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342006026 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342006027 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342006028 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 1427342006029 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1427342006030 active site 1427342006031 catalytic triad [active] 1427342006032 dimer interface [polypeptide binding]; other site 1427342006033 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342006034 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 1427342006035 active site 1427342006036 FMN binding site [chemical binding]; other site 1427342006037 2,4-decadienoyl-CoA binding site; other site 1427342006038 catalytic residue [active] 1427342006039 4Fe-4S cluster binding site [ion binding]; other site 1427342006040 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342006041 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 1427342006042 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 1427342006043 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01231 1427342006044 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 1427342006045 Pseudomonas aeruginosa PA3087 and related proteins, metallophosphatase domain; Region: MPP_PA3087; cd07413 1427342006046 active site 1427342006047 metal binding site [ion binding]; metal-binding site 1427342006048 Rhomboid family; Region: Rhomboid; pfam01694 1427342006049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3139 1427342006050 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 1427342006051 aminopeptidase N; Provisional; Region: pepN; PRK14015 1427342006052 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 1427342006053 active site 1427342006054 Zn binding site [ion binding]; other site 1427342006055 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 1427342006056 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 1427342006057 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 1427342006058 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 1427342006059 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342006060 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342006061 dimer interface [polypeptide binding]; other site 1427342006062 phosphorylation site [posttranslational modification] 1427342006063 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342006064 ATP binding site [chemical binding]; other site 1427342006065 Mg2+ binding site [ion binding]; other site 1427342006066 G-X-G motif; other site 1427342006067 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342006068 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006069 active site 1427342006070 phosphorylation site [posttranslational modification] 1427342006071 intermolecular recognition site; other site 1427342006072 dimerization interface [polypeptide binding]; other site 1427342006073 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342006074 DNA binding site [nucleotide binding] 1427342006075 chlorophyllase; Region: PLN00021 1427342006076 Oxygen tolerance; Region: BatD; pfam13584 1427342006077 von Willebrand factor type A domain; Region: VWA_2; pfam13519 1427342006078 metal ion-dependent adhesion site (MIDAS); other site 1427342006079 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342006080 TPR repeat; Region: TPR_11; pfam13414 1427342006081 binding surface 1427342006082 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 1427342006083 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 1427342006084 metal ion-dependent adhesion site (MIDAS); other site 1427342006085 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 1427342006086 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 1427342006087 Protein of unknown function DUF58; Region: DUF58; pfam01882 1427342006088 MoxR-like ATPases [General function prediction only]; Region: COG0714 1427342006089 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 1427342006090 Walker A motif; other site 1427342006091 ATP binding site [chemical binding]; other site 1427342006092 Walker B motif; other site 1427342006093 arginine finger; other site 1427342006094 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 1427342006095 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1427342006096 Uncharacterized conserved protein [Function unknown]; Region: COG3868 1427342006097 C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria; Region: CE4_PelA_like_C; cd10922 1427342006098 putative active site [active] 1427342006099 Tetratricopeptide repeat; Region: TPR_15; pfam13429 1427342006100 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 1427342006101 GAF domain; Region: GAF_3; pfam13492 1427342006102 HEAT repeats; Region: HEAT_2; pfam13646 1427342006103 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_3; cd03813 1427342006104 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342006105 Predicted membrane protein [Function unknown]; Region: COG4267 1427342006106 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1427342006107 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342006108 non-specific DNA binding site [nucleotide binding]; other site 1427342006109 salt bridge; other site 1427342006110 sequence-specific DNA binding site [nucleotide binding]; other site 1427342006111 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342006112 non-specific DNA binding site [nucleotide binding]; other site 1427342006113 salt bridge; other site 1427342006114 sequence-specific DNA binding site [nucleotide binding]; other site 1427342006115 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 1427342006116 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 1427342006117 putative active site [active] 1427342006118 Zn binding site [ion binding]; other site 1427342006119 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342006120 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342006121 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1427342006122 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 1427342006123 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 1427342006124 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 1427342006125 quinone interaction residues [chemical binding]; other site 1427342006126 active site 1427342006127 catalytic residues [active] 1427342006128 FMN binding site [chemical binding]; other site 1427342006129 substrate binding site [chemical binding]; other site 1427342006130 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 1427342006131 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 1427342006132 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 1427342006133 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342006134 S-adenosylmethionine binding site [chemical binding]; other site 1427342006135 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 1427342006136 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 1427342006137 hypothetical protein; Provisional; Region: PRK11702 1427342006138 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342006139 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006140 active site 1427342006141 phosphorylation site [posttranslational modification] 1427342006142 intermolecular recognition site; other site 1427342006143 dimerization interface [polypeptide binding]; other site 1427342006144 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342006145 DNA binding residues [nucleotide binding] 1427342006146 dimerization interface [polypeptide binding]; other site 1427342006147 PAS domain; Region: PAS_9; pfam13426 1427342006148 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342006149 dimer interface [polypeptide binding]; other site 1427342006150 phosphorylation site [posttranslational modification] 1427342006151 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342006152 ATP binding site [chemical binding]; other site 1427342006153 Mg2+ binding site [ion binding]; other site 1427342006154 G-X-G motif; other site 1427342006155 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342006156 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006157 active site 1427342006158 phosphorylation site [posttranslational modification] 1427342006159 intermolecular recognition site; other site 1427342006160 dimerization interface [polypeptide binding]; other site 1427342006161 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342006162 putative binding surface; other site 1427342006163 active site 1427342006164 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 1427342006165 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342006166 Zn2+ binding site [ion binding]; other site 1427342006167 Mg2+ binding site [ion binding]; other site 1427342006168 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1427342006169 Predicted membrane protein [Function unknown]; Region: COG5393 1427342006170 Uncharacterized conserved protein [Function unknown]; Region: ElaB; COG4575 1427342006171 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 1427342006172 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342006173 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342006174 Predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase [General function prediction only]; Region: COG3576 1427342006175 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342006176 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 1427342006177 putative C-terminal domain interface [polypeptide binding]; other site 1427342006178 putative GSH binding site (G-site) [chemical binding]; other site 1427342006179 putative dimer interface [polypeptide binding]; other site 1427342006180 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 1427342006181 putative N-terminal domain interface [polypeptide binding]; other site 1427342006182 putative dimer interface [polypeptide binding]; other site 1427342006183 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342006184 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006185 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006186 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 1427342006187 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 1427342006188 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342006189 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 1427342006190 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 1427342006191 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 1427342006192 GTP binding site; other site 1427342006193 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 1427342006194 MPT binding site; other site 1427342006195 trimer interface [polypeptide binding]; other site 1427342006196 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 1427342006197 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 1427342006198 dimer interface [polypeptide binding]; other site 1427342006199 putative functional site; other site 1427342006200 putative MPT binding site; other site 1427342006201 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342006202 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342006203 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342006204 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1427342006205 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342006206 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 1427342006207 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 1427342006208 uncharacterized ygcE-like proteins; Region: FGGY_ygcE_like; cd07779 1427342006209 putative N- and C-terminal domain interface [polypeptide binding]; other site 1427342006210 putative active site [active] 1427342006211 MgATP binding site [chemical binding]; other site 1427342006212 catalytic site [active] 1427342006213 metal binding site [ion binding]; metal-binding site 1427342006214 putative carbohydrate binding site [chemical binding]; other site 1427342006215 lipid kinase; Reviewed; Region: PRK13054 1427342006216 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 1427342006217 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 1427342006218 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 1427342006219 MOSC domain; Region: MOSC; pfam03473 1427342006220 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 1427342006221 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1427342006222 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342006223 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342006224 catalytic residue [active] 1427342006225 ABC transporter ATPase component; Reviewed; Region: PRK11147 1427342006226 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342006227 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342006228 ABC transporter; Region: ABC_tran_2; pfam12848 1427342006229 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342006230 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342006231 Ligand Binding Site [chemical binding]; other site 1427342006232 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 1427342006233 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 1427342006234 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342006235 substrate binding site [chemical binding]; other site 1427342006236 oxyanion hole (OAH) forming residues; other site 1427342006237 trimer interface [polypeptide binding]; other site 1427342006238 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342006239 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342006240 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 1427342006241 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342006242 dimer interface [polypeptide binding]; other site 1427342006243 active site 1427342006244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4728 1427342006245 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 1427342006246 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 1427342006247 active site 1427342006248 interdomain interaction site; other site 1427342006249 putative metal-binding site [ion binding]; other site 1427342006250 nucleotide binding site [chemical binding]; other site 1427342006251 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 1427342006252 domain I; other site 1427342006253 DNA binding groove [nucleotide binding] 1427342006254 phosphate binding site [ion binding]; other site 1427342006255 domain II; other site 1427342006256 domain III; other site 1427342006257 nucleotide binding site [chemical binding]; other site 1427342006258 catalytic site [active] 1427342006259 domain IV; other site 1427342006260 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1427342006261 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1427342006262 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 1427342006263 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 1427342006264 SOS-response cell division inhibitor, blocks FtsZ ring formation [Cell division and chromosome partitioning]; Region: SulA; COG5404 1427342006265 LexA repressor; Validated; Region: PRK00215 1427342006266 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 1427342006267 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1427342006268 Catalytic site [active] 1427342006269 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006270 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006271 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1427342006272 beta-hexosaminidase; Provisional; Region: PRK05337 1427342006273 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 1427342006274 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 1427342006275 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1427342006276 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1427342006277 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342006278 ATP binding site [chemical binding]; other site 1427342006279 putative Mg++ binding site [ion binding]; other site 1427342006280 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342006281 nucleotide binding region [chemical binding]; other site 1427342006282 ATP-binding site [chemical binding]; other site 1427342006283 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1427342006284 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 1427342006285 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 1427342006286 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1427342006287 aromatic amino acid transporter; Provisional; Region: PRK10238 1427342006288 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 1427342006289 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342006290 E3 interaction surface; other site 1427342006291 lipoyl attachment site [posttranslational modification]; other site 1427342006292 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 1427342006293 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 1427342006294 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 1427342006295 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 1427342006296 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 1427342006297 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 1427342006298 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 1427342006299 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342006300 catalytic loop [active] 1427342006301 iron binding site [ion binding]; other site 1427342006302 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 1427342006303 FAD binding pocket [chemical binding]; other site 1427342006304 FAD binding motif [chemical binding]; other site 1427342006305 phosphate binding motif [ion binding]; other site 1427342006306 beta-alpha-beta structure motif; other site 1427342006307 NAD binding pocket [chemical binding]; other site 1427342006308 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 1427342006309 ApbE family; Region: ApbE; pfam02424 1427342006310 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2991 1427342006311 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 1427342006312 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342006313 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342006314 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1427342006315 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 1427342006316 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 1427342006317 active site 1427342006318 catalytic site [active] 1427342006319 metal binding site [ion binding]; metal-binding site 1427342006320 PilZ domain; Region: PilZ; pfam07238 1427342006321 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1427342006322 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1427342006323 FtsX-like permease family; Region: FtsX; pfam02687 1427342006324 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 1427342006325 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342006326 Walker A/P-loop; other site 1427342006327 ATP binding site [chemical binding]; other site 1427342006328 Q-loop/lid; other site 1427342006329 ABC transporter signature motif; other site 1427342006330 Walker B; other site 1427342006331 D-loop; other site 1427342006332 H-loop/switch region; other site 1427342006333 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1427342006334 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1427342006335 FtsX-like permease family; Region: FtsX; pfam02687 1427342006336 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3216 1427342006337 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 1427342006338 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 1427342006339 Competence protein; Region: Competence; pfam03772 1427342006340 Competence protein; Region: Competence; cl00471 1427342006341 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1427342006342 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 1427342006343 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1427342006344 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1427342006345 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1427342006346 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1427342006347 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1427342006348 Uncharacterized conserved protein [Function unknown]; Region: COG2835 1427342006349 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1427342006350 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1427342006351 Ligand binding site; other site 1427342006352 oligomer interface; other site 1427342006353 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1427342006354 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1427342006355 active site 1427342006356 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 1427342006357 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342006358 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1427342006359 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 1427342006360 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 1427342006361 homodimer interface [polypeptide binding]; other site 1427342006362 oligonucleotide binding site [chemical binding]; other site 1427342006363 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 1427342006364 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342006365 RNA binding surface [nucleotide binding]; other site 1427342006366 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1427342006367 active site 1427342006368 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 1427342006369 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342006370 motif II; other site 1427342006371 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1427342006372 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1427342006373 tandem repeat interface [polypeptide binding]; other site 1427342006374 oligomer interface [polypeptide binding]; other site 1427342006375 active site residues [active] 1427342006376 Maf-like protein; Region: Maf; pfam02545 1427342006377 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 1427342006378 active site 1427342006379 dimer interface [polypeptide binding]; other site 1427342006380 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 1427342006381 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 1427342006382 putative phosphate acyltransferase; Provisional; Region: PRK05331 1427342006383 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1427342006384 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1427342006385 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1427342006386 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1427342006387 NAD(P) binding site [chemical binding]; other site 1427342006388 homotetramer interface [polypeptide binding]; other site 1427342006389 homodimer interface [polypeptide binding]; other site 1427342006390 active site 1427342006391 acyl carrier protein; Provisional; Region: acpP; PRK00982 1427342006392 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1427342006393 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 1427342006394 dimer interface [polypeptide binding]; other site 1427342006395 active site 1427342006396 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1427342006397 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 1427342006398 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342006399 catalytic residue [active] 1427342006400 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1427342006401 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1427342006402 dimerization interface [polypeptide binding]; other site 1427342006403 thymidylate kinase; Validated; Region: tmk; PRK00698 1427342006404 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 1427342006405 TMP-binding site; other site 1427342006406 ATP-binding site [chemical binding]; other site 1427342006407 DNA polymerase III subunit delta'; Validated; Region: PRK05707 1427342006408 DNA polymerase III subunit delta'; Validated; Region: PRK08485 1427342006409 PilZ domain; Region: PilZ; cl01260 1427342006410 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1427342006411 active site 1427342006412 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1427342006413 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342006414 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342006415 catalytic residue [active] 1427342006416 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006417 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006418 WHG domain; Region: WHG; pfam13305 1427342006419 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342006420 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1427342006421 FeS/SAM binding site; other site 1427342006422 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3816 1427342006423 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 1427342006424 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 1427342006425 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342006426 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 1427342006427 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 1427342006428 Ligand binding site [chemical binding]; other site 1427342006429 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1427342006430 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 1427342006431 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1427342006432 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342006433 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 1427342006434 active site 1427342006435 Int/Topo IB signature motif; other site 1427342006436 DNA binding site [nucleotide binding] 1427342006437 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1427342006438 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 1427342006439 Integrase core domain; Region: rve; pfam00665 1427342006440 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 1427342006441 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 1427342006442 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 1427342006443 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342006444 Walker A motif; other site 1427342006445 ATP binding site [chemical binding]; other site 1427342006446 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1427342006447 hypothetical protein; Reviewed; Region: PRK00024 1427342006448 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1427342006449 MPN+ (JAMM) motif; other site 1427342006450 Zinc-binding site [ion binding]; other site 1427342006451 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 1427342006452 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342006453 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 1427342006454 ArsC family; Region: ArsC; pfam03960 1427342006455 catalytic residues [active] 1427342006456 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 1427342006457 arsenical-resistance protein; Region: acr3; TIGR00832 1427342006458 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 1427342006459 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 1427342006460 P loop; other site 1427342006461 Nucleotide binding site [chemical binding]; other site 1427342006462 DTAP/Switch II; other site 1427342006463 Switch I; other site 1427342006464 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 1427342006465 DTAP/Switch II; other site 1427342006466 Switch I; other site 1427342006467 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 1427342006468 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1427342006469 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1427342006470 active site 1427342006471 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 1427342006472 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342006473 putative metal binding site [ion binding]; other site 1427342006474 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342006475 putative DNA binding site [nucleotide binding]; other site 1427342006476 putative Zn2+ binding site [ion binding]; other site 1427342006477 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 1427342006478 Domain of unknown function (DUF932); Region: DUF932; pfam06067 1427342006479 ParB-like nuclease domain; Region: ParBc; pfam02195 1427342006480 Uncharacterized conserved protein [Function unknown]; Region: COG5489 1427342006481 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1427342006482 sequence-specific DNA binding site [nucleotide binding]; other site 1427342006483 salt bridge; other site 1427342006484 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 1427342006485 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 1427342006486 Helix-turn-helix domain; Region: HTH_17; cl17695 1427342006487 Replication initiator protein A; Region: RPA; cl17860 1427342006488 ParA-like protein; Provisional; Region: PHA02518 1427342006489 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342006490 P-loop; other site 1427342006491 Magnesium ion binding site [ion binding]; other site 1427342006492 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 1427342006493 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 1427342006494 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 1427342006495 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 1427342006496 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 1427342006497 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 1427342006498 Transposase; Region: DDE_Tnp_ISL3; pfam01610 1427342006499 Predicted permease; Region: DUF318; cl17795 1427342006500 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006501 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006502 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342006503 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342006504 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342006505 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1427342006506 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342006507 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 1427342006508 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006509 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342006510 dimerization interface [polypeptide binding]; other site 1427342006511 substrate binding pocket [chemical binding]; other site 1427342006512 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 1427342006513 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342006514 Walker A motif; other site 1427342006515 ATP binding site [chemical binding]; other site 1427342006516 Walker B motif; other site 1427342006517 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 1427342006518 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1427342006519 ATP binding site [chemical binding]; other site 1427342006520 Walker A motif; other site 1427342006521 hexamer interface [polypeptide binding]; other site 1427342006522 Walker B motif; other site 1427342006523 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1427342006524 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 1427342006525 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 1427342006526 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1427342006527 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342006528 Walker A motif; other site 1427342006529 ATP binding site [chemical binding]; other site 1427342006530 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 1427342006531 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 1427342006532 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 1427342006533 conjugal transfer protein TrbL; Provisional; Region: PRK13875 1427342006534 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1427342006535 conjugal transfer protein TrbF; Provisional; Region: PRK13872 1427342006536 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1427342006537 VirB7 interaction site; other site 1427342006538 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1427342006539 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 1427342006540 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 1427342006541 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 1427342006542 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 1427342006543 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 1427342006544 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 1427342006545 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342006546 nucleophilic elbow; other site 1427342006547 catalytic triad; other site 1427342006548 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 1427342006549 active site 1427342006550 SAM binding site [chemical binding]; other site 1427342006551 homodimer interface [polypeptide binding]; other site 1427342006552 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 1427342006553 Predicted integral membrane protein [Function unknown]; Region: COG5446 1427342006554 Probable cobalt transporter subunit (CbtB); Region: CbtB; pfam09489 1427342006555 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 1427342006556 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 1427342006557 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 1427342006558 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 1427342006559 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 1427342006560 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 1427342006561 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 1427342006562 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1427342006563 magnesium chelatase ATPase subunit I; Region: BchI-ChlI; TIGR02030 1427342006564 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342006565 Walker A motif; other site 1427342006566 ATP binding site [chemical binding]; other site 1427342006567 Walker B motif; other site 1427342006568 arginine finger; other site 1427342006569 Mg-chelatase subunit ChlD [Coenzyme metabolism]; Region: ChlD; COG1240 1427342006570 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 1427342006571 metal ion-dependent adhesion site (MIDAS); other site 1427342006572 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342006573 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 1427342006574 dimer interface [polypeptide binding]; other site 1427342006575 active site 1427342006576 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 1427342006577 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1427342006578 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cd00538 1427342006579 PA/protease or protease-like domain interface [polypeptide binding]; other site 1427342006580 M28 Zn-peptidase Streptomyces griseus Aminopeptidase and similar proteins; Region: M28_SGAP_like; cd03876 1427342006581 active site 1427342006582 metal binding site [ion binding]; metal-binding site 1427342006583 xanthine permease; Region: pbuX; TIGR03173 1427342006584 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1427342006585 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342006586 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342006587 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342006588 putative substrate translocation pore; other site 1427342006589 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342006590 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 1427342006591 FMN binding site [chemical binding]; other site 1427342006592 active site 1427342006593 substrate binding site [chemical binding]; other site 1427342006594 catalytic residue [active] 1427342006595 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006596 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006597 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006598 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006599 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342006600 dimerization interface [polypeptide binding]; other site 1427342006601 LysE type translocator; Region: LysE; cl00565 1427342006602 Serine hydrolase; Region: Ser_hydrolase; cl17834 1427342006603 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342006604 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 1427342006605 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342006606 Walker A/P-loop; other site 1427342006607 ATP binding site [chemical binding]; other site 1427342006608 Q-loop/lid; other site 1427342006609 ABC transporter signature motif; other site 1427342006610 Walker B; other site 1427342006611 D-loop; other site 1427342006612 H-loop/switch region; other site 1427342006613 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342006614 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342006615 dimer interface [polypeptide binding]; other site 1427342006616 conserved gate region; other site 1427342006617 putative PBP binding loops; other site 1427342006618 ABC-ATPase subunit interface; other site 1427342006619 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342006620 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342006621 dimer interface [polypeptide binding]; other site 1427342006622 conserved gate region; other site 1427342006623 putative PBP binding loops; other site 1427342006624 ABC-ATPase subunit interface; other site 1427342006625 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 1427342006626 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342006627 substrate binding pocket [chemical binding]; other site 1427342006628 membrane-bound complex binding site; other site 1427342006629 hinge residues; other site 1427342006630 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1427342006631 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 1427342006632 metal binding site [ion binding]; metal-binding site 1427342006633 putative dimer interface [polypeptide binding]; other site 1427342006634 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 1427342006635 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006636 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342006637 dimerization interface [polypeptide binding]; other site 1427342006638 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342006639 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342006640 dimerization interface [polypeptide binding]; other site 1427342006641 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342006642 dimer interface [polypeptide binding]; other site 1427342006643 putative CheW interface [polypeptide binding]; other site 1427342006644 short chain dehydrogenase; Provisional; Region: PRK12744 1427342006645 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342006646 NAD(P) binding site [chemical binding]; other site 1427342006647 active site 1427342006648 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342006649 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342006650 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342006651 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342006652 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1427342006653 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1427342006654 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 1427342006655 ABC-ATPase subunit interface; other site 1427342006656 dimer interface [polypeptide binding]; other site 1427342006657 putative PBP binding regions; other site 1427342006658 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 1427342006659 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 1427342006660 putative ligand binding residues [chemical binding]; other site 1427342006661 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1427342006662 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342006663 Walker A/P-loop; other site 1427342006664 ATP binding site [chemical binding]; other site 1427342006665 Q-loop/lid; other site 1427342006666 ABC transporter signature motif; other site 1427342006667 Walker B; other site 1427342006668 H-loop/switch region; other site 1427342006669 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342006670 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342006671 N-terminal plug; other site 1427342006672 ligand-binding site [chemical binding]; other site 1427342006673 Predicted membrane protein [Function unknown]; Region: COG1971 1427342006674 Domain of unknown function DUF; Region: DUF204; pfam02659 1427342006675 Domain of unknown function DUF; Region: DUF204; pfam02659 1427342006676 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 1427342006677 cobalt-precorrin-6x reductase; Reviewed; Region: PRK08057 1427342006678 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 1427342006679 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 1427342006680 active site 1427342006681 putative homodimer interface [polypeptide binding]; other site 1427342006682 SAM binding site [chemical binding]; other site 1427342006683 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 1427342006684 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342006685 S-adenosylmethionine binding site [chemical binding]; other site 1427342006686 precorrin-3B synthase; Region: CobG; TIGR02435 1427342006687 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342006688 precorrin-8X methylmutase; Reviewed; Region: cobH; PRK08285 1427342006689 Precorrin-8X methylmutase; Region: CbiC; pfam02570 1427342006690 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 1427342006691 homodimer interface [polypeptide binding]; other site 1427342006692 active site 1427342006693 SAM binding site [chemical binding]; other site 1427342006694 Cobalamin biosynthesis protein CbiG [Coenzyme metabolism]; Region: CbiG; COG2073 1427342006695 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 1427342006696 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 1427342006697 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 1427342006698 active site 1427342006699 SAM binding site [chemical binding]; other site 1427342006700 homodimer interface [polypeptide binding]; other site 1427342006701 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342006702 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342006703 substrate binding pocket [chemical binding]; other site 1427342006704 membrane-bound complex binding site; other site 1427342006705 hinge residues; other site 1427342006706 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 1427342006707 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342006708 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342006709 ligand binding site [chemical binding]; other site 1427342006710 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342006711 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006712 active site 1427342006713 phosphorylation site [posttranslational modification] 1427342006714 intermolecular recognition site; other site 1427342006715 dimerization interface [polypeptide binding]; other site 1427342006716 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342006717 DNA binding residues [nucleotide binding] 1427342006718 dimerization interface [polypeptide binding]; other site 1427342006719 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342006720 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342006721 DNA-binding site [nucleotide binding]; DNA binding site 1427342006722 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342006723 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342006724 homodimer interface [polypeptide binding]; other site 1427342006725 catalytic residue [active] 1427342006726 RNA polymerase sigma factor; Provisional; Region: PRK12513 1427342006727 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342006728 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342006729 DNA binding residues [nucleotide binding] 1427342006730 long-chain-acyl-CoA synthetase; Validated; Region: PRK08279 1427342006731 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342006732 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342006733 Fatty acid transport proteins (FATP) play dual roles as fatty acid transporters and its activation enzymes; Region: FATP_FACS; cd05940 1427342006734 acyl-activating enzyme (AAE) consensus motif; other site 1427342006735 acyl-activating enzyme (AAE) consensus motif; other site 1427342006736 putative AMP binding site [chemical binding]; other site 1427342006737 putative active site [active] 1427342006738 putative CoA binding site [chemical binding]; other site 1427342006739 short chain dehydrogenase; Provisional; Region: PRK08278 1427342006740 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342006741 NAD(P) binding site [chemical binding]; other site 1427342006742 active site 1427342006743 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1427342006744 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342006745 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1427342006746 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 1427342006747 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342006748 carboxyltransferase (CT) interaction site; other site 1427342006749 biotinylation site [posttranslational modification]; other site 1427342006750 enoyl-CoA hydratase; Provisional; Region: PRK05995 1427342006751 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342006752 substrate binding site [chemical binding]; other site 1427342006753 oxyanion hole (OAH) forming residues; other site 1427342006754 trimer interface [polypeptide binding]; other site 1427342006755 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342006756 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342006757 active site 1427342006758 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1427342006759 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1427342006760 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1427342006761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342006762 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342006763 NAD(P) binding site [chemical binding]; other site 1427342006764 active site 1427342006765 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 1427342006766 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342006767 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342006768 CAAX protease self-immunity; Region: Abi; pfam02517 1427342006769 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 1427342006770 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 1427342006771 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342006772 ATP binding site [chemical binding]; other site 1427342006773 Mg2+ binding site [ion binding]; other site 1427342006774 G-X-G motif; other site 1427342006775 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342006776 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006777 active site 1427342006778 phosphorylation site [posttranslational modification] 1427342006779 intermolecular recognition site; other site 1427342006780 dimerization interface [polypeptide binding]; other site 1427342006781 Predicted membrane protein [Function unknown]; Region: COG4125 1427342006782 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 1427342006783 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 1427342006784 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006785 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006786 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342006787 dimerization interface [polypeptide binding]; other site 1427342006788 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 1427342006789 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006790 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006791 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 1427342006792 putative effector binding pocket; other site 1427342006793 putative dimerization interface [polypeptide binding]; other site 1427342006794 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 1427342006795 active site 1427342006796 dimer interface [polypeptide binding]; other site 1427342006797 MoxR-like ATPases [General function prediction only]; Region: COG0714 1427342006798 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342006799 Walker A motif; other site 1427342006800 ATP binding site [chemical binding]; other site 1427342006801 Walker B motif; other site 1427342006802 arginine finger; other site 1427342006803 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 1427342006804 Protein of unknown function DUF58; Region: DUF58; pfam01882 1427342006805 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 1427342006806 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1427342006807 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1427342006808 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 1427342006809 Uncharacterized conserved protein [Function unknown]; Region: COG5607 1427342006810 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 1427342006811 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 1427342006812 active site 1427342006813 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342006814 active site 2 [active] 1427342006815 active site 1 [active] 1427342006816 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342006817 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342006818 metal binding site [ion binding]; metal-binding site 1427342006819 active site 1427342006820 I-site; other site 1427342006821 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 1427342006822 Phage terminase, small subunit [DNA replication, recombination, and repair]; Region: XtmA; COG3728 1427342006823 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342006824 dimerization interface [polypeptide binding]; other site 1427342006825 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342006826 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342006827 dimer interface [polypeptide binding]; other site 1427342006828 putative CheW interface [polypeptide binding]; other site 1427342006829 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1427342006830 active site 1427342006831 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]; Region: COG4623 1427342006832 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342006833 substrate binding pocket [chemical binding]; other site 1427342006834 membrane-bound complex binding site; other site 1427342006835 hinge residues; other site 1427342006836 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342006837 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342006838 catalytic residue [active] 1427342006839 Predicted membrane protein [Function unknown]; Region: COG2259 1427342006840 lipase chaperone; Provisional; Region: PRK01294 1427342006841 Lipase chaperone [Posttranslational modification, protein turnover, chaperones]; Region: LimK; COG5380 1427342006842 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 1427342006843 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 1427342006844 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 1427342006845 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 1427342006846 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1427342006847 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1427342006848 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 1427342006849 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 1427342006850 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342006851 Walker A/P-loop; other site 1427342006852 ATP binding site [chemical binding]; other site 1427342006853 Q-loop/lid; other site 1427342006854 ABC transporter signature motif; other site 1427342006855 Walker B; other site 1427342006856 D-loop; other site 1427342006857 H-loop/switch region; other site 1427342006858 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 1427342006859 active site 1427342006860 catalytic triad [active] 1427342006861 oxyanion hole [active] 1427342006862 switch loop; other site 1427342006863 L,D-transpeptidase; Provisional; Region: PRK10260 1427342006864 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 1427342006865 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1427342006866 Protein of unknown function (DUF3359); Region: DUF3359; pfam11839 1427342006867 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 1427342006868 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 1427342006869 elongation factor P; Validated; Region: PRK00529 1427342006870 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1427342006871 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 1427342006872 RNA binding site [nucleotide binding]; other site 1427342006873 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 1427342006874 RNA binding site [nucleotide binding]; other site 1427342006875 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 1427342006876 Transcriptional regulators [Transcription]; Region: MarR; COG1846 1427342006877 MarR family; Region: MarR; pfam01047 1427342006878 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006879 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006880 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342006881 putative effector binding pocket; other site 1427342006882 dimerization interface [polypeptide binding]; other site 1427342006883 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1427342006884 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006885 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006886 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342006887 dimerization interface [polypeptide binding]; other site 1427342006888 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 1427342006889 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 1427342006890 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 1427342006891 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 1427342006892 Spermidine synthase [Amino acid transport and metabolism]; Region: SpeE; COG0421 1427342006893 enoyl-CoA hydratase; Provisional; Region: PRK06563 1427342006894 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342006895 substrate binding site [chemical binding]; other site 1427342006896 oxyanion hole (OAH) forming residues; other site 1427342006897 trimer interface [polypeptide binding]; other site 1427342006898 helicase 45; Provisional; Region: PTZ00424 1427342006899 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 1427342006900 ATP binding site [chemical binding]; other site 1427342006901 Mg++ binding site [ion binding]; other site 1427342006902 motif III; other site 1427342006903 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342006904 nucleotide binding region [chemical binding]; other site 1427342006905 ATP-binding site [chemical binding]; other site 1427342006906 DbpA RNA binding domain; Region: DbpA; pfam03880 1427342006907 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 1427342006908 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 1427342006909 putative active site [active] 1427342006910 metal binding site [ion binding]; metal-binding site 1427342006911 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006912 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006913 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342006914 putative effector binding pocket; other site 1427342006915 dimerization interface [polypeptide binding]; other site 1427342006916 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342006917 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 1427342006918 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342006919 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342006920 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342006921 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342006922 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006923 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342006924 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 1427342006925 putative substrate binding pocket [chemical binding]; other site 1427342006926 putative dimerization interface [polypeptide binding]; other site 1427342006927 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342006928 Ligand Binding Site [chemical binding]; other site 1427342006929 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 1427342006930 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 1427342006931 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 1427342006932 putative active site [active] 1427342006933 Zn binding site [ion binding]; other site 1427342006934 heat shock protein HtpX; Provisional; Region: PRK05457 1427342006935 aminotransferase AlaT; Validated; Region: PRK09265 1427342006936 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342006937 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342006938 homodimer interface [polypeptide binding]; other site 1427342006939 catalytic residue [active] 1427342006940 methionine sulfoxide reductase B; Provisional; Region: PRK00222 1427342006941 SelR domain; Region: SelR; pfam01641 1427342006942 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 1427342006943 catalytic residues [active] 1427342006944 dimer interface [polypeptide binding]; other site 1427342006945 MarR family; Region: MarR_2; cl17246 1427342006946 Transcriptional regulators [Transcription]; Region: MarR; COG1846 1427342006947 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 1427342006948 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342006949 ATP binding site [chemical binding]; other site 1427342006950 Mg2+ binding site [ion binding]; other site 1427342006951 G-X-G motif; other site 1427342006952 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342006953 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342006954 active site 1427342006955 phosphorylation site [posttranslational modification] 1427342006956 intermolecular recognition site; other site 1427342006957 dimerization interface [polypeptide binding]; other site 1427342006958 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 1427342006959 Protein of unknown function (DUF815); Region: DUF815; pfam05673 1427342006960 Walker A motif; other site 1427342006961 ATP binding site [chemical binding]; other site 1427342006962 Walker B motif; other site 1427342006963 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 1427342006964 GAF domain; Region: GAF_2; pfam13185 1427342006965 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342006966 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1427342006967 C-terminal domain interface [polypeptide binding]; other site 1427342006968 GSH binding site (G-site) [chemical binding]; other site 1427342006969 dimer interface [polypeptide binding]; other site 1427342006970 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1427342006971 N-terminal domain interface [polypeptide binding]; other site 1427342006972 dimer interface [polypeptide binding]; other site 1427342006973 substrate binding pocket (H-site) [chemical binding]; other site 1427342006974 integrase; Provisional; Region: PRK09692 1427342006975 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 1427342006976 active site 1427342006977 Int/Topo IB signature motif; other site 1427342006978 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 1427342006979 Helix-turn-helix domain; Region: HTH_38; pfam13936 1427342006980 Helix-turn-helix domain; Region: HTH_17; pfam12728 1427342006981 Integrase core domain; Region: rve; pfam00665 1427342006982 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 1427342006983 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342006984 Walker A motif; other site 1427342006985 ATP binding site [chemical binding]; other site 1427342006986 Walker B motif; other site 1427342006987 arginine finger; other site 1427342006988 Outer membrane efflux protein; Region: OEP; pfam02321 1427342006989 Outer membrane efflux protein; Region: OEP; pfam02321 1427342006990 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 1427342006991 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1427342006992 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 1427342006993 Transposase; Region: HTH_Tnp_1; pfam01527 1427342006994 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342006995 HTH-like domain; Region: HTH_21; pfam13276 1427342006996 Integrase core domain; Region: rve; pfam00665 1427342006997 Integrase core domain; Region: rve_3; pfam13683 1427342006998 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342006999 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342007000 Copper resistance protein K; Region: CopK; pfam11525 1427342007001 Putative copper export protein [Inorganic ion transport and metabolism]; Region: PcoD; COG1276 1427342007002 CopC domain; Region: CopC; pfam04234 1427342007003 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 1427342007004 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 1427342007005 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342007006 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342007007 motif II; other site 1427342007008 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 1427342007009 Predicted metal-binding protein [General function prediction only]; Region: COG3019 1427342007010 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 1427342007011 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 1427342007012 Multicopper oxidase; Region: Cu-oxidase; pfam00394 1427342007013 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 1427342007014 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342007015 DNA binding site [nucleotide binding] 1427342007016 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342007017 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007018 dimerization interface [polypeptide binding]; other site 1427342007019 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342007020 dimer interface [polypeptide binding]; other site 1427342007021 phosphorylation site [posttranslational modification] 1427342007022 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007023 ATP binding site [chemical binding]; other site 1427342007024 Mg2+ binding site [ion binding]; other site 1427342007025 G-X-G motif; other site 1427342007026 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342007027 putative DNA binding site [nucleotide binding]; other site 1427342007028 putative Zn2+ binding site [ion binding]; other site 1427342007029 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 1427342007030 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342007031 putative metal binding site [ion binding]; other site 1427342007032 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1427342007033 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1427342007034 active site 1427342007035 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 1427342007036 arsenical-resistance protein; Region: acr3; TIGR00832 1427342007037 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 1427342007038 ArsC family; Region: ArsC; pfam03960 1427342007039 catalytic residues [active] 1427342007040 Predicted transcriptional regulators [Transcription]; Region: COG1695 1427342007041 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 1427342007042 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 1427342007043 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 1427342007044 Chromate transporter; Region: Chromate_transp; pfam02417 1427342007045 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342007046 Coenzyme A binding pocket [chemical binding]; other site 1427342007047 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1427342007048 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342007049 HlyD family secretion protein; Region: HlyD; pfam00529 1427342007050 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342007051 Putative helicase; Region: TraI_2; pfam07514 1427342007052 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 1427342007053 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 1427342007054 RES domain; Region: RES; smart00953 1427342007055 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 1427342007056 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 1427342007057 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 1427342007058 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 1427342007059 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1427342007060 MPN+ (JAMM) motif; other site 1427342007061 Zinc-binding site [ion binding]; other site 1427342007062 Thioredoxin; Region: Thioredoxin_4; cl17273 1427342007063 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 1427342007064 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 1427342007065 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 1427342007066 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 1427342007067 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 1427342007068 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 1427342007069 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 1427342007070 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 1427342007071 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 1427342007072 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 1427342007073 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 1427342007074 DNA binding domain, excisionase family; Region: excise; TIGR01764 1427342007075 PIN domain; Region: PIN_3; pfam13470 1427342007076 ATPase family associated with various cellular activities (AAA); Region: AAA; pfam00004 1427342007077 HORMA domain; Region: HORMA; pfam02301 1427342007078 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 1427342007079 active site 1427342007080 NTP binding site [chemical binding]; other site 1427342007081 metal binding triad [ion binding]; metal-binding site 1427342007082 AAA domain; Region: AAA_23; pfam13476 1427342007083 P-loop containing region of AAA domain; Region: AAA_29; cl17516 1427342007084 AAA domain; Region: AAA_21; pfam13304 1427342007085 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342007086 ABC transporter signature motif; other site 1427342007087 Walker B; other site 1427342007088 D-loop; other site 1427342007089 H-loop/switch region; other site 1427342007090 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 1427342007091 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 1427342007092 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 1427342007093 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 1427342007094 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342007095 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342007096 catalytic residue [active] 1427342007097 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 1427342007098 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 1427342007099 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1427342007100 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342007101 nucleotide binding region [chemical binding]; other site 1427342007102 ATP-binding site [chemical binding]; other site 1427342007103 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1427342007104 S-adenosylmethionine binding site [chemical binding]; other site 1427342007105 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 1427342007106 Domain of unknown function (DUF932); Region: DUF932; pfam06067 1427342007107 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 1427342007108 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 1427342007109 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 1427342007110 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 1427342007111 putative mercuric reductase; Provisional; Region: PRK13748 1427342007112 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342007113 metal-binding site [ion binding] 1427342007114 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342007115 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342007116 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1427342007117 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342007118 metal-binding site [ion binding] 1427342007119 putative mercuric transport protein; Provisional; Region: PRK13751 1427342007120 putative transcriptional regulator MerR; Provisional; Region: PRK13752 1427342007121 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 1427342007122 DNA binding residues [nucleotide binding] 1427342007123 dimer interface [polypeptide binding]; other site 1427342007124 mercury binding site [ion binding]; other site 1427342007125 Herpesvirus UL36 tegument protein; Region: Herpes_UL36; pfam03586 1427342007126 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1427342007127 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342007128 metal-binding site [ion binding] 1427342007129 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342007130 metal-binding site [ion binding] 1427342007131 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 1427342007132 metal-binding site [ion binding] 1427342007133 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1427342007134 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342007135 metal-binding site [ion binding] 1427342007136 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342007137 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 1427342007138 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 1427342007139 DNA binding residues [nucleotide binding] 1427342007140 dimer interface [polypeptide binding]; other site 1427342007141 putative metal binding site [ion binding]; other site 1427342007142 Cation efflux family; Region: Cation_efflux; cl00316 1427342007143 DNA topoisomerase III; Provisional; Region: PRK07726 1427342007144 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 1427342007145 active site 1427342007146 putative interdomain interaction site [polypeptide binding]; other site 1427342007147 putative metal-binding site [ion binding]; other site 1427342007148 putative nucleotide binding site [chemical binding]; other site 1427342007149 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 1427342007150 domain I; other site 1427342007151 DNA binding groove [nucleotide binding] 1427342007152 phosphate binding site [ion binding]; other site 1427342007153 domain II; other site 1427342007154 domain III; other site 1427342007155 nucleotide binding site [chemical binding]; other site 1427342007156 catalytic site [active] 1427342007157 domain IV; other site 1427342007158 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1427342007159 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1427342007160 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 1427342007161 dimer interface [polypeptide binding]; other site 1427342007162 ssDNA binding site [nucleotide binding]; other site 1427342007163 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1427342007164 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 1427342007165 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 1427342007166 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 1427342007167 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 1427342007168 ParB-like nuclease domain; Region: ParBc; pfam02195 1427342007169 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1427342007170 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342007171 Magnesium ion binding site [ion binding]; other site 1427342007172 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 1427342007173 Killing trait; Region: RebB; pfam11747 1427342007174 Killing trait; Region: RebB; pfam11747 1427342007175 Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; Region: PheS; COG0016 1427342007176 Killing trait; Region: RebB; pfam11747 1427342007177 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1427342007178 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 1427342007179 DNA binding residues [nucleotide binding] 1427342007180 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1427342007181 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342007182 ligand binding site [chemical binding]; other site 1427342007183 flexible hinge region; other site 1427342007184 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 1427342007185 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 1427342007186 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 1427342007187 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 1427342007188 active site 1427342007189 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 1427342007190 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1427342007191 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1427342007192 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342007193 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 1427342007194 putative C-terminal domain interface [polypeptide binding]; other site 1427342007195 putative GSH binding site (G-site) [chemical binding]; other site 1427342007196 putative dimer interface [polypeptide binding]; other site 1427342007197 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 1427342007198 putative N-terminal domain interface [polypeptide binding]; other site 1427342007199 putative dimer interface [polypeptide binding]; other site 1427342007200 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342007201 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1427342007202 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342007203 Walker A/P-loop; other site 1427342007204 ATP binding site [chemical binding]; other site 1427342007205 Q-loop/lid; other site 1427342007206 ABC transporter signature motif; other site 1427342007207 Walker B; other site 1427342007208 D-loop; other site 1427342007209 H-loop/switch region; other site 1427342007210 inner membrane transport permease; Provisional; Region: PRK15066 1427342007211 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1427342007212 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 1427342007213 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007214 dimerization interface [polypeptide binding]; other site 1427342007215 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342007216 dimer interface [polypeptide binding]; other site 1427342007217 phosphorylation site [posttranslational modification] 1427342007218 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007219 ATP binding site [chemical binding]; other site 1427342007220 Mg2+ binding site [ion binding]; other site 1427342007221 G-X-G motif; other site 1427342007222 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 1427342007223 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007224 active site 1427342007225 phosphorylation site [posttranslational modification] 1427342007226 intermolecular recognition site; other site 1427342007227 dimerization interface [polypeptide binding]; other site 1427342007228 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342007229 DNA binding site [nucleotide binding] 1427342007230 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 1427342007231 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 1427342007232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1427342007233 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1427342007234 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1427342007235 Domain of unknown function (DUF4404); Region: DUF4404; pfam14357 1427342007236 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342007237 Zn2+ binding site [ion binding]; other site 1427342007238 Mg2+ binding site [ion binding]; other site 1427342007239 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 1427342007240 transcriptional regulator protein; Region: phnR; TIGR03337 1427342007241 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342007242 DNA-binding site [nucleotide binding]; DNA binding site 1427342007243 UTRA domain; Region: UTRA; pfam07702 1427342007244 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342007245 active site 1427342007246 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1427342007247 PilZ domain; Region: PilZ; pfam07238 1427342007248 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342007249 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007250 active site 1427342007251 phosphorylation site [posttranslational modification] 1427342007252 intermolecular recognition site; other site 1427342007253 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 1427342007254 dimerization interface [polypeptide binding]; other site 1427342007255 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 1427342007256 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 1427342007257 anti sigma factor interaction site; other site 1427342007258 regulatory phosphorylation site [posttranslational modification]; other site 1427342007259 transaldolase-like protein; Provisional; Region: PTZ00411 1427342007260 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 1427342007261 active site 1427342007262 dimer interface [polypeptide binding]; other site 1427342007263 catalytic residue [active] 1427342007264 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 1427342007265 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 1427342007266 FMN binding site [chemical binding]; other site 1427342007267 active site 1427342007268 catalytic residues [active] 1427342007269 substrate binding site [chemical binding]; other site 1427342007270 Right handed beta helix region; Region: Beta_helix; pfam13229 1427342007271 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 1427342007272 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342007273 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342007274 dimer interface [polypeptide binding]; other site 1427342007275 putative CheW interface [polypeptide binding]; other site 1427342007276 glutamate carboxypeptidase; Reviewed; Region: PRK06133 1427342007277 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 1427342007278 metal binding site [ion binding]; metal-binding site 1427342007279 dimer interface [polypeptide binding]; other site 1427342007280 GAF domain; Region: GAF_2; pfam13185 1427342007281 Predicted transcriptional regulator [Transcription]; Region: COG3655 1427342007282 salt bridge; other site 1427342007283 non-specific DNA binding site [nucleotide binding]; other site 1427342007284 sequence-specific DNA binding site [nucleotide binding]; other site 1427342007285 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 1427342007286 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_3; pfam13582 1427342007287 active site 1427342007288 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 1427342007289 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 1427342007290 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39A; cd02549 1427342007291 putative active site [active] 1427342007292 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 1427342007293 binding surface 1427342007294 Formate/nitrite family of transporters [Inorganic ion transport and metabolism]; Region: FocA; COG2116 1427342007295 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342007296 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342007297 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 1427342007298 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 1427342007299 GAF domain; Region: GAF; pfam01590 1427342007300 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342007301 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342007302 metal binding site [ion binding]; metal-binding site 1427342007303 active site 1427342007304 I-site; other site 1427342007305 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 1427342007306 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 1427342007307 nudix motif; other site 1427342007308 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 1427342007309 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342007310 substrate binding site [chemical binding]; other site 1427342007311 oxyanion hole (OAH) forming residues; other site 1427342007312 trimer interface [polypeptide binding]; other site 1427342007313 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 1427342007314 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342007315 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342007316 Dyp-type peroxidase family; Region: Dyp_perox; pfam04261 1427342007317 Serine hydrolase; Region: Ser_hydrolase; cl17834 1427342007318 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342007319 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 1427342007320 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342007321 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342007322 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342007323 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342007324 dimerization interface [polypeptide binding]; other site 1427342007325 Predicted membrane protein [Function unknown]; Region: COG4125 1427342007326 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 1427342007327 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 1427342007328 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 1427342007329 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1427342007330 secondary substrate binding site; other site 1427342007331 primary substrate binding site; other site 1427342007332 inhibition loop; other site 1427342007333 dimerization interface [polypeptide binding]; other site 1427342007334 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 1427342007335 Uncharacterized conserved protein [Function unknown]; Region: ElaB; COG4575 1427342007336 Predicted membrane protein [Function unknown]; Region: COG1238 1427342007337 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 1427342007338 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 1427342007339 Endonuclease I [DNA replication, recombination, and repair]; Region: EndA; COG2356 1427342007340 DNA-specific endonuclease I; Provisional; Region: PRK15137 1427342007341 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 1427342007342 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 1427342007343 active site 1427342007344 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 1427342007345 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342007346 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1427342007347 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 1427342007348 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 1427342007349 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 1427342007350 active site 1427342007351 dimer interface [polypeptide binding]; other site 1427342007352 motif 1; other site 1427342007353 motif 2; other site 1427342007354 motif 3; other site 1427342007355 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 1427342007356 anticodon binding site; other site 1427342007357 translation initiation factor IF-3; Region: infC; TIGR00168 1427342007358 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1427342007359 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1427342007360 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1427342007361 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1427342007362 23S rRNA binding site [nucleotide binding]; other site 1427342007363 L21 binding site [polypeptide binding]; other site 1427342007364 L13 binding site [polypeptide binding]; other site 1427342007365 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1427342007366 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1427342007367 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 1427342007368 dimer interface [polypeptide binding]; other site 1427342007369 motif 1; other site 1427342007370 active site 1427342007371 motif 2; other site 1427342007372 motif 3; other site 1427342007373 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1427342007374 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 1427342007375 putative tRNA-binding site [nucleotide binding]; other site 1427342007376 B3/4 domain; Region: B3_4; pfam03483 1427342007377 tRNA synthetase B5 domain; Region: B5; smart00874 1427342007378 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 1427342007379 dimer interface [polypeptide binding]; other site 1427342007380 motif 1; other site 1427342007381 motif 3; other site 1427342007382 motif 2; other site 1427342007383 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1427342007384 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 1427342007385 IHF dimer interface [polypeptide binding]; other site 1427342007386 IHF - DNA interface [nucleotide binding]; other site 1427342007387 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 1427342007388 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1427342007389 DNA binding residues [nucleotide binding] 1427342007390 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342007391 ATP binding site [chemical binding]; other site 1427342007392 putative Mg++ binding site [ion binding]; other site 1427342007393 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342007394 nucleotide binding region [chemical binding]; other site 1427342007395 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 1427342007396 ATP-binding site [chemical binding]; other site 1427342007397 AIPR protein; Region: AIPR; pfam10592 1427342007398 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1427342007399 DNA methylase; Region: N6_N4_Mtase; pfam01555 1427342007400 DNA methylase; Region: N6_N4_Mtase; cl17433 1427342007401 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1427342007402 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1427342007403 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1427342007404 Protein of unknown function DUF262; Region: DUF262; pfam03235 1427342007405 Protein of unknown function DUF262; Region: DUF262; pfam03235 1427342007406 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1427342007407 Uncharacterized conserved protein [Function unknown]; Region: COG3586 1427342007408 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342007409 HTH-like domain; Region: HTH_21; pfam13276 1427342007410 Integrase core domain; Region: rve; pfam00665 1427342007411 Integrase core domain; Region: rve_3; pfam13683 1427342007412 Transposase; Region: HTH_Tnp_1; pfam01527 1427342007413 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 1427342007414 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1427342007415 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 1427342007416 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 1427342007417 Transposase; Region: HTH_Tnp_1; pfam01527 1427342007418 HTH-like domain; Region: HTH_21; pfam13276 1427342007419 Protein of unknown function (DUF2699); Region: DUF2699; pfam10919 1427342007420 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 1427342007421 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1427342007422 active site 1427342007423 ATP binding site [chemical binding]; other site 1427342007424 substrate binding site [chemical binding]; other site 1427342007425 activation loop (A-loop); other site 1427342007426 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 1427342007427 AAA domain; Region: AAA_11; pfam13086 1427342007428 Part of AAA domain; Region: AAA_19; pfam13245 1427342007429 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 1427342007430 AAA domain; Region: AAA_12; pfam13087 1427342007431 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 1427342007432 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 1427342007433 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 1427342007434 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007435 Walker A motif; other site 1427342007436 ATP binding site [chemical binding]; other site 1427342007437 Walker B motif; other site 1427342007438 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1427342007439 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1427342007440 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 1427342007441 dimer interface [polypeptide binding]; other site 1427342007442 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 1427342007443 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 1427342007444 potential catalytic triad [active] 1427342007445 conserved cys residue [active] 1427342007446 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1427342007447 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1427342007448 DNA binding residues [nucleotide binding] 1427342007449 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342007450 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342007451 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342007452 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342007453 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 1427342007454 putative active site [active] 1427342007455 putative FMN binding site [chemical binding]; other site 1427342007456 putative substrate binding site [chemical binding]; other site 1427342007457 putative catalytic residue [active] 1427342007458 Ferredoxin [Energy production and conversion]; Region: COG1146 1427342007459 4Fe-4S binding domain; Region: Fer4; cl02805 1427342007460 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 1427342007461 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 1427342007462 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_1; cd02762 1427342007463 putative [Fe4-S4] binding site [ion binding]; other site 1427342007464 putative molybdopterin cofactor binding site [chemical binding]; other site 1427342007465 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342007466 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_1; cd02782 1427342007467 putative molybdopterin cofactor binding site; other site 1427342007468 Predicted transcriptional regulators [Transcription]; Region: COG1733 1427342007469 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 1427342007470 Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen...; Region: KU; cl02666 1427342007471 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342007472 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342007473 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342007474 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1427342007475 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 1427342007476 dimer interface [polypeptide binding]; other site 1427342007477 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342007478 catalytic residue [active] 1427342007479 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 1427342007480 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1427342007481 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007482 Walker A motif; other site 1427342007483 ATP binding site [chemical binding]; other site 1427342007484 Walker B motif; other site 1427342007485 arginine finger; other site 1427342007486 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1427342007487 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 1427342007488 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342007489 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342007490 Tse2 immunity protein Tsi2 and similar proteins; Region: Tsi2_like; cd11690 1427342007491 dimer interface [polypeptide binding]; other site 1427342007492 Transmembrane secretion effector; Region: MFS_3; pfam05977 1427342007493 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342007494 putative substrate translocation pore; other site 1427342007495 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342007496 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 1427342007497 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 1427342007498 active site 1427342007499 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1427342007500 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342007501 catalytic triad [active] 1427342007502 dimer interface [polypeptide binding]; other site 1427342007503 conserved cis-peptide bond; other site 1427342007504 Protein of unknown function (DUF1427); Region: DUF1427; cl01771 1427342007505 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342007506 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342007507 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342007508 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 1427342007509 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 1427342007510 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342007511 catalytic residues [active] 1427342007512 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 1427342007513 Predicted transcriptional regulator [Transcription]; Region: COG1959 1427342007514 Transcriptional regulator; Region: Rrf2; pfam02082 1427342007515 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 1427342007516 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342007517 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 1427342007518 outer membrane receptor FepA; Provisional; Region: PRK13524 1427342007519 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342007520 N-terminal plug; other site 1427342007521 ligand-binding site [chemical binding]; other site 1427342007522 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342007523 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342007524 phosphorylation site [posttranslational modification] 1427342007525 dimer interface [polypeptide binding]; other site 1427342007526 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007527 ATP binding site [chemical binding]; other site 1427342007528 Mg2+ binding site [ion binding]; other site 1427342007529 G-X-G motif; other site 1427342007530 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342007531 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007532 active site 1427342007533 phosphorylation site [posttranslational modification] 1427342007534 intermolecular recognition site; other site 1427342007535 dimerization interface [polypeptide binding]; other site 1427342007536 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342007537 DNA binding site [nucleotide binding] 1427342007538 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342007539 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342007540 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342007541 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 1427342007542 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 1427342007543 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1427342007544 RHS Repeat; Region: RHS_repeat; pfam05593 1427342007545 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1427342007546 RHS Repeat; Region: RHS_repeat; pfam05593 1427342007547 YD repeat (two copies); Region: YD_repeat_2x; TIGR01643 1427342007548 RHS Repeat; Region: RHS_repeat; pfam05593 1427342007549 RHS Repeat; Region: RHS_repeat; cl11982 1427342007550 RHS protein; Region: RHS; pfam03527 1427342007551 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 1427342007552 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1427342007553 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1427342007554 tetramer interface [polypeptide binding]; other site 1427342007555 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342007556 catalytic residue [active] 1427342007557 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 1427342007558 SnoaL-like domain; Region: SnoaL_2; pfam12680 1427342007559 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342007560 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342007561 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342007562 putative effector binding pocket; other site 1427342007563 dimerization interface [polypeptide binding]; other site 1427342007564 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 1427342007565 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 1427342007566 NADP binding site [chemical binding]; other site 1427342007567 dimer interface [polypeptide binding]; other site 1427342007568 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342007569 S-adenosylmethionine binding site [chemical binding]; other site 1427342007570 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1427342007571 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1427342007572 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 1427342007573 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 1427342007574 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 1427342007575 Walker A motif; other site 1427342007576 ATP binding site [chemical binding]; other site 1427342007577 Walker B motif; other site 1427342007578 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 1427342007579 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342007580 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342007581 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 1427342007582 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 1427342007583 putative active site [active] 1427342007584 putative NTP binding site [chemical binding]; other site 1427342007585 putative nucleic acid binding site [nucleotide binding]; other site 1427342007586 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 1427342007587 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 1427342007588 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1427342007589 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 1427342007590 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 1427342007591 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 1427342007592 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1427342007593 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1427342007594 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 1427342007595 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1427342007596 active site 1427342007597 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 1427342007598 GAF domain; Region: GAF; pfam01590 1427342007599 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007600 Walker A motif; other site 1427342007601 ATP binding site [chemical binding]; other site 1427342007602 Walker B motif; other site 1427342007603 arginine finger; other site 1427342007604 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 1427342007605 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 1427342007606 heme-binding site [chemical binding]; other site 1427342007607 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 1427342007608 FAD binding pocket [chemical binding]; other site 1427342007609 FAD binding motif [chemical binding]; other site 1427342007610 phosphate binding motif [ion binding]; other site 1427342007611 beta-alpha-beta structure motif; other site 1427342007612 NAD binding pocket [chemical binding]; other site 1427342007613 Heme binding pocket [chemical binding]; other site 1427342007614 Uncharacterized protein involved in response to NO [Inorganic ion transport and metabolism]; Region: NnrS; COG3213 1427342007615 hypothetical protein; Provisional; Region: PRK10318 1427342007616 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1427342007617 Predicted membrane protein [Function unknown]; Region: COG3212 1427342007618 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1427342007619 Predicted membrane protein [Function unknown]; Region: COG3212 1427342007620 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342007621 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007622 active site 1427342007623 phosphorylation site [posttranslational modification] 1427342007624 intermolecular recognition site; other site 1427342007625 dimerization interface [polypeptide binding]; other site 1427342007626 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342007627 DNA binding site [nucleotide binding] 1427342007628 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342007629 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007630 ATP binding site [chemical binding]; other site 1427342007631 Mg2+ binding site [ion binding]; other site 1427342007632 G-X-G motif; other site 1427342007633 Cache domain; Region: Cache_1; pfam02743 1427342007634 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007635 dimerization interface [polypeptide binding]; other site 1427342007636 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342007637 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342007638 dimer interface [polypeptide binding]; other site 1427342007639 putative CheW interface [polypeptide binding]; other site 1427342007640 Predicted permease [General function prediction only]; Region: COG2056 1427342007641 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 1427342007642 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 1427342007643 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007644 dimerization interface [polypeptide binding]; other site 1427342007645 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342007646 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342007647 dimer interface [polypeptide binding]; other site 1427342007648 putative CheW interface [polypeptide binding]; other site 1427342007649 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1427342007650 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1427342007651 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342007652 S-adenosylmethionine binding site [chemical binding]; other site 1427342007653 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 1427342007654 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1427342007655 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1427342007656 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1427342007657 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1427342007658 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1427342007659 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1427342007660 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1427342007661 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 1427342007662 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 1427342007663 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1427342007664 4Fe-4S binding domain; Region: Fer4; pfam00037 1427342007665 4Fe-4S binding domain; Region: Fer4; pfam00037 1427342007666 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1427342007667 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 1427342007668 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342007669 catalytic loop [active] 1427342007670 iron binding site [ion binding]; other site 1427342007671 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1427342007672 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 1427342007673 [4Fe-4S] binding site [ion binding]; other site 1427342007674 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 1427342007675 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 1427342007676 SLBB domain; Region: SLBB; pfam10531 1427342007677 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 1427342007678 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1427342007679 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 1427342007680 putative dimer interface [polypeptide binding]; other site 1427342007681 [2Fe-2S] cluster binding site [ion binding]; other site 1427342007682 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 1427342007683 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1427342007684 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1427342007685 NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]; Region: NuoB; COG0377 1427342007686 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1427342007687 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342007688 CoenzymeA binding site [chemical binding]; other site 1427342007689 subunit interaction site [polypeptide binding]; other site 1427342007690 PHB binding site; other site 1427342007691 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 1427342007692 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 1427342007693 tetramer interface [polypeptide binding]; other site 1427342007694 active site 1427342007695 Mg2+/Mn2+ binding site [ion binding]; other site 1427342007696 isocitrate lyase; Region: PLN02892 1427342007697 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342007698 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342007699 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342007700 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342007701 Coenzyme A binding pocket [chemical binding]; other site 1427342007702 Uncharacterized conserved protein [Function unknown]; Region: COG2850 1427342007703 Cupin domain; Region: Cupin_2; cl17218 1427342007704 adenylosuccinate lyase; Provisional; Region: PRK09285 1427342007705 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 1427342007706 tetramer interface [polypeptide binding]; other site 1427342007707 active site 1427342007708 EamA-like transporter family; Region: EamA; pfam00892 1427342007709 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1427342007710 Uncharacterized protein involved in purine metabolism [General function prediction only]; Region: COG2915 1427342007711 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1427342007712 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs; Region: tRNA_Me_trans; cd01998 1427342007713 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 1427342007714 nudix motif; other site 1427342007715 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 1427342007716 Monomeric isocitrate dehydrogenase; Region: IDH; pfam03971 1427342007717 isocitrate dehydrogenase; Validated; Region: PRK07362 1427342007718 isocitrate dehydrogenase; Reviewed; Region: PRK07006 1427342007719 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342007720 DNA-binding site [nucleotide binding]; DNA binding site 1427342007721 RNA-binding motif; other site 1427342007722 ATP-dependent Clp protease adaptor protein ClpS; Reviewed; Region: clpS; PRK00033 1427342007723 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 1427342007724 Clp amino terminal domain; Region: Clp_N; pfam02861 1427342007725 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007726 Walker A motif; other site 1427342007727 ATP binding site [chemical binding]; other site 1427342007728 Walker B motif; other site 1427342007729 arginine finger; other site 1427342007730 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007731 Walker A motif; other site 1427342007732 ATP binding site [chemical binding]; other site 1427342007733 Walker B motif; other site 1427342007734 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1427342007735 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 1427342007736 rRNA binding site [nucleotide binding]; other site 1427342007737 predicted 30S ribosome binding site; other site 1427342007738 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 1427342007739 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 1427342007740 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 1427342007741 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 1427342007742 thioredoxin reductase; Provisional; Region: PRK10262 1427342007743 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342007744 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342007745 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1427342007746 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1427342007747 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1427342007748 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1427342007749 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1427342007750 recombination factor protein RarA; Reviewed; Region: PRK13342 1427342007751 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342007752 Walker A motif; other site 1427342007753 ATP binding site [chemical binding]; other site 1427342007754 Walker B motif; other site 1427342007755 arginine finger; other site 1427342007756 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 1427342007757 seryl-tRNA synthetase; Provisional; Region: PRK05431 1427342007758 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1427342007759 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 1427342007760 dimer interface [polypeptide binding]; other site 1427342007761 active site 1427342007762 motif 1; other site 1427342007763 motif 2; other site 1427342007764 motif 3; other site 1427342007765 siroheme synthase; Provisional; Region: cysG; PRK10637 1427342007766 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 1427342007767 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 1427342007768 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 1427342007769 active site 1427342007770 SAM binding site [chemical binding]; other site 1427342007771 homodimer interface [polypeptide binding]; other site 1427342007772 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 1427342007773 Glutathione S-transferase, N-terminal domain; Region: GST_N_2; pfam13409 1427342007774 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 1427342007775 putative dimer interface [polypeptide binding]; other site 1427342007776 N-terminal domain interface [polypeptide binding]; other site 1427342007777 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342007778 hypothetical protein; Validated; Region: PRK09071 1427342007779 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1427342007780 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 1427342007781 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 1427342007782 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 1427342007783 sulfur relay protein TusC; Validated; Region: PRK00211 1427342007784 sulfur transfer complex subunit TusD; Validated; Region: PRK00207 1427342007785 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1427342007786 YccA-like proteins; Region: YccA_like; cd10433 1427342007787 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative...; Region: 4RHOD_Repeat_1; cd01532 1427342007788 active site residue [active] 1427342007789 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic...; Region: 4RHOD_Repeat_2; cd01533 1427342007790 active site residue [active] 1427342007791 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 1427342007792 active site residue [active] 1427342007793 Member of the Rhodanese Homology Domain superfamily, repeat 4. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative...; Region: 4RHOD_Repeat_4; cd01535 1427342007794 active site residue [active] 1427342007795 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 1427342007796 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342007797 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342007798 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342007799 dimerization interface [polypeptide binding]; other site 1427342007800 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342007801 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 1427342007802 dimer interface [polypeptide binding]; other site 1427342007803 active site 1427342007804 non-prolyl cis peptide bond; other site 1427342007805 insertion regions; other site 1427342007806 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342007807 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007808 substrate binding pocket [chemical binding]; other site 1427342007809 membrane-bound complex binding site; other site 1427342007810 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342007811 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 1427342007812 dimer interface [polypeptide binding]; other site 1427342007813 active site 1427342007814 non-prolyl cis peptide bond; other site 1427342007815 insertion regions; other site 1427342007816 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342007817 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 1427342007818 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342007819 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007820 substrate binding pocket [chemical binding]; other site 1427342007821 membrane-bound complex binding site; other site 1427342007822 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007823 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342007824 membrane-bound complex binding site; other site 1427342007825 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 1427342007826 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007827 substrate binding pocket [chemical binding]; other site 1427342007828 membrane-bound complex binding site; other site 1427342007829 hinge residues; other site 1427342007830 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342007831 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342007832 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342007833 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342007834 DNA binding residues [nucleotide binding] 1427342007835 dimerization interface [polypeptide binding]; other site 1427342007836 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342007837 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342007838 N-terminal plug; other site 1427342007839 ligand-binding site [chemical binding]; other site 1427342007840 oxalate/formate antiporter; Region: oxa_formateAnti; TIGR04259 1427342007841 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 1427342007842 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342007843 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342007844 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342007845 hypothetical protein; Provisional; Region: PRK06753 1427342007846 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342007847 response regulator; Provisional; Region: PRK09483 1427342007848 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007849 active site 1427342007850 phosphorylation site [posttranslational modification] 1427342007851 intermolecular recognition site; other site 1427342007852 dimerization interface [polypeptide binding]; other site 1427342007853 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342007854 DNA binding residues [nucleotide binding] 1427342007855 dimerization interface [polypeptide binding]; other site 1427342007856 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1427342007857 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1427342007858 GIY-YIG motif/motif A; other site 1427342007859 active site 1427342007860 catalytic site [active] 1427342007861 putative DNA binding site [nucleotide binding]; other site 1427342007862 metal binding site [ion binding]; metal-binding site 1427342007863 UvrB/uvrC motif; Region: UVR; pfam02151 1427342007864 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1427342007865 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 1427342007866 DNA binding site [nucleotide binding] 1427342007867 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1427342007868 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1427342007869 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007870 substrate binding pocket [chemical binding]; other site 1427342007871 membrane-bound complex binding site; other site 1427342007872 hinge residues; other site 1427342007873 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342007874 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342007875 substrate binding pocket [chemical binding]; other site 1427342007876 membrane-bound complex binding site; other site 1427342007877 hinge residues; other site 1427342007878 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342007879 dimer interface [polypeptide binding]; other site 1427342007880 phosphorylation site [posttranslational modification] 1427342007881 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007882 ATP binding site [chemical binding]; other site 1427342007883 Mg2+ binding site [ion binding]; other site 1427342007884 G-X-G motif; other site 1427342007885 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342007886 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007887 active site 1427342007888 phosphorylation site [posttranslational modification] 1427342007889 intermolecular recognition site; other site 1427342007890 dimerization interface [polypeptide binding]; other site 1427342007891 Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]; Region: ProQ; COG3109 1427342007892 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cd00236 1427342007893 putative RNA binding sites [nucleotide binding]; other site 1427342007894 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1427342007895 Tryptophan 2,3-dioxygenase (vermilion) [Amino acid transport and metabolism]; Region: TDO2; COG3483 1427342007896 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 1427342007897 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342007898 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342007899 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 1427342007900 putative DNA binding site [nucleotide binding]; other site 1427342007901 putative Zn2+ binding site [ion binding]; other site 1427342007902 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342007903 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1427342007904 EamA-like transporter family; Region: EamA; pfam00892 1427342007905 EamA-like transporter family; Region: EamA; pfam00892 1427342007906 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 1427342007907 dimer interface [polypeptide binding]; other site 1427342007908 FMN binding site [chemical binding]; other site 1427342007909 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 1427342007910 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1427342007911 Di-iron ligands [ion binding]; other site 1427342007912 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342007913 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007914 dimerization interface [polypeptide binding]; other site 1427342007915 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342007916 dimer interface [polypeptide binding]; other site 1427342007917 putative CheW interface [polypeptide binding]; other site 1427342007918 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 1427342007919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342007920 active site 1427342007921 phosphorylation site [posttranslational modification] 1427342007922 intermolecular recognition site; other site 1427342007923 dimerization interface [polypeptide binding]; other site 1427342007924 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342007925 Zn2+ binding site [ion binding]; other site 1427342007926 Mg2+ binding site [ion binding]; other site 1427342007927 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342007928 ATP binding site [chemical binding]; other site 1427342007929 Mg2+ binding site [ion binding]; other site 1427342007930 G-X-G motif; other site 1427342007931 GAF domain; Region: GAF; pfam01590 1427342007932 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 1427342007933 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342007934 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342007935 metal binding site [ion binding]; metal-binding site 1427342007936 active site 1427342007937 I-site; other site 1427342007938 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342007939 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342007940 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 1427342007941 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342007942 S-adenosylmethionine binding site [chemical binding]; other site 1427342007943 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1427342007944 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 1427342007945 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1427342007946 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 1427342007947 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 1427342007948 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342007949 dimerization interface [polypeptide binding]; other site 1427342007950 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342007951 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342007952 dimer interface [polypeptide binding]; other site 1427342007953 putative CheW interface [polypeptide binding]; other site 1427342007954 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 1427342007955 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 1427342007956 MgtC family; Region: MgtC; pfam02308 1427342007957 AMP-binding domain protein; Validated; Region: PRK08315 1427342007958 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342007959 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 1427342007960 acyl-activating enzyme (AAE) consensus motif; other site 1427342007961 putative AMP binding site [chemical binding]; other site 1427342007962 putative active site [active] 1427342007963 putative CoA binding site [chemical binding]; other site 1427342007964 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342007965 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342007966 SurA N-terminal domain; Region: SurA_N; pfam09312 1427342007967 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342007968 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 1427342007969 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342007970 acyl-activating enzyme (AAE) consensus motif; other site 1427342007971 AMP binding site [chemical binding]; other site 1427342007972 active site 1427342007973 CoA binding site [chemical binding]; other site 1427342007974 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 1427342007975 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 1427342007976 NAD binding site [chemical binding]; other site 1427342007977 homodimer interface [polypeptide binding]; other site 1427342007978 homotetramer interface [polypeptide binding]; other site 1427342007979 active site 1427342007980 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 1427342007981 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342007982 dimer interface [polypeptide binding]; other site 1427342007983 active site 1427342007984 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342007985 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342007986 active site 1427342007987 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 1427342007988 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342007989 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 1427342007990 substrate binding pocket [chemical binding]; other site 1427342007991 dimerization interface [polypeptide binding]; other site 1427342007992 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342007993 Acyl-CoA dehydrogenases similar to fadE2; Region: ACAD_FadE2; cd01155 1427342007994 FAD binding site [chemical binding]; other site 1427342007995 substrate binding site [chemical binding]; other site 1427342007996 catalytic base [active] 1427342007997 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 1427342007998 ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PstS; COG0226 1427342007999 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 1427342008000 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342008001 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342008002 ligand binding site [chemical binding]; other site 1427342008003 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008004 LysR family transcriptional regulator; Provisional; Region: PRK14997 1427342008005 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342008006 putative effector binding pocket; other site 1427342008007 dimerization interface [polypeptide binding]; other site 1427342008008 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 1427342008009 dimer interface [polypeptide binding]; other site 1427342008010 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342008011 metal binding site [ion binding]; metal-binding site 1427342008012 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1427342008013 putative catalytic site [active] 1427342008014 putative phosphate binding site [ion binding]; other site 1427342008015 active site 1427342008016 metal binding site A [ion binding]; metal-binding site 1427342008017 DNA binding site [nucleotide binding] 1427342008018 putative AP binding site [nucleotide binding]; other site 1427342008019 putative metal binding site B [ion binding]; other site 1427342008020 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1427342008021 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342008022 Coenzyme A binding pocket [chemical binding]; other site 1427342008023 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 1427342008024 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342008025 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1427342008026 Surface antigen; Region: Bac_surface_Ag; pfam01103 1427342008027 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 1427342008028 Family of unknown function (DUF490); Region: DUF490; pfam04357 1427342008029 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 1427342008030 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1427342008031 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342008032 Putative methyltransferase; Region: Methyltransf_20; pfam12147 1427342008033 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 1427342008034 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1427342008035 active site 1427342008036 Predicted protein-tyrosine phosphatase [Signal transduction mechanisms]; Region: CDC14; COG2453 1427342008037 active site 1427342008038 catalytic residues [active] 1427342008039 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342008040 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1427342008041 putative acyl-acceptor binding pocket; other site 1427342008042 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 1427342008043 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1427342008044 Mor transcription activator family; Region: Mor; cl02360 1427342008045 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 1427342008046 Protein of unknown function (DUF2786); Region: DUF2786; pfam10979 1427342008047 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 1427342008048 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 1427342008049 AAA ATPase domain; Region: AAA_16; pfam13191 1427342008050 Integrase core domain; Region: rve; pfam00665 1427342008051 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342008052 putative DNA binding site [nucleotide binding]; other site 1427342008053 putative Zn2+ binding site [ion binding]; other site 1427342008054 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 1427342008055 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 1427342008056 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342008057 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342008058 catalytic residue [active] 1427342008059 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 1427342008060 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 1427342008061 Terminase-like family; Region: Terminase_6; pfam03237 1427342008062 Protein of unknown function (DUF935); Region: DUF935; pfam06074 1427342008063 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 1427342008064 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 1427342008065 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 1427342008066 Gp37 protein; Region: Gp37; pfam09646 1427342008067 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1427342008068 tape measure domain; Region: tape_meas_nterm; TIGR02675 1427342008069 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 1427342008070 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 1427342008071 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1427342008072 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1427342008073 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 1427342008074 Putative phage tail protein; Region: Phage-tail_3; pfam13550 1427342008075 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342008076 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342008077 active site 1427342008078 catalytic tetrad [active] 1427342008079 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008080 LysR family transcriptional regulator; Provisional; Region: PRK14997 1427342008081 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 1427342008082 putative effector binding pocket; other site 1427342008083 putative dimerization interface [polypeptide binding]; other site 1427342008084 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1427342008085 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1427342008086 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 1427342008087 dimer interface [polypeptide binding]; other site 1427342008088 catalytic triad [active] 1427342008089 peroxidatic and resolving cysteines [active] 1427342008090 putative aminotransferase; Provisional; Region: PRK09105 1427342008091 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342008092 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342008093 homodimer interface [polypeptide binding]; other site 1427342008094 catalytic residue [active] 1427342008095 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 1427342008096 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 1427342008097 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342008098 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342008099 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342008100 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1427342008101 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342008102 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; cl02090 1427342008103 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1427342008104 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342008105 synaptic vesicle protein SV2; Region: synapt_SV2; TIGR01299 1427342008106 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 1427342008107 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342008108 dimerization interface [polypeptide binding]; other site 1427342008109 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342008110 dimer interface [polypeptide binding]; other site 1427342008111 phosphorylation site [posttranslational modification] 1427342008112 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342008113 ATP binding site [chemical binding]; other site 1427342008114 Mg2+ binding site [ion binding]; other site 1427342008115 G-X-G motif; other site 1427342008116 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 1427342008117 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342008118 active site 1427342008119 phosphorylation site [posttranslational modification] 1427342008120 intermolecular recognition site; other site 1427342008121 dimerization interface [polypeptide binding]; other site 1427342008122 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342008123 DNA binding site [nucleotide binding] 1427342008124 Outer membrane efflux protein; Region: OEP; pfam02321 1427342008125 Outer membrane efflux protein; Region: OEP; pfam02321 1427342008126 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342008127 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 1427342008128 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342008129 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 1427342008130 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342008131 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008132 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342008133 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008134 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 1427342008135 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 1427342008136 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 1427342008137 putative alpha subunit interface [polypeptide binding]; other site 1427342008138 putative active site [active] 1427342008139 putative substrate binding site [chemical binding]; other site 1427342008140 Fe binding site [ion binding]; other site 1427342008141 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 1427342008142 inter-subunit interface; other site 1427342008143 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 1427342008144 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342008145 catalytic loop [active] 1427342008146 iron binding site [ion binding]; other site 1427342008147 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 1427342008148 FAD binding pocket [chemical binding]; other site 1427342008149 FAD binding motif [chemical binding]; other site 1427342008150 phosphate binding motif [ion binding]; other site 1427342008151 beta-alpha-beta structure motif; other site 1427342008152 NAD binding pocket [chemical binding]; other site 1427342008153 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional; Region: benD; PRK12823 1427342008154 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 1427342008155 putative NAD(P) binding site [chemical binding]; other site 1427342008156 active site 1427342008157 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 1427342008158 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342008159 catalytic loop [active] 1427342008160 iron binding site [ion binding]; other site 1427342008161 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 1427342008162 FAD binding pocket [chemical binding]; other site 1427342008163 FAD binding motif [chemical binding]; other site 1427342008164 phosphate binding motif [ion binding]; other site 1427342008165 beta-alpha-beta structure motif; other site 1427342008166 NAD binding pocket [chemical binding]; other site 1427342008167 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 1427342008168 inter-subunit interface; other site 1427342008169 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 1427342008170 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 1427342008171 [2Fe-2S] cluster binding site [ion binding]; other site 1427342008172 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 1427342008173 putative alpha subunit interface [polypeptide binding]; other site 1427342008174 putative active site [active] 1427342008175 putative substrate binding site [chemical binding]; other site 1427342008176 Fe binding site [ion binding]; other site 1427342008177 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342008178 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 1427342008179 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008180 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342008181 dimerization interface [polypeptide binding]; other site 1427342008182 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 1427342008183 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 1427342008184 octamer interface [polypeptide binding]; other site 1427342008185 active site 1427342008186 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CatC1; COG4829 1427342008187 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 1427342008188 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 1427342008189 dimer interface [polypeptide binding]; other site 1427342008190 active site 1427342008191 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342008192 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4859 1427342008193 Leucine rich repeat; Region: LRR_8; pfam13855 1427342008194 Leucine rich repeat; Region: LRR_8; pfam13855 1427342008195 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1427342008196 active site 1427342008197 ATP binding site [chemical binding]; other site 1427342008198 substrate binding site [chemical binding]; other site 1427342008199 activation loop (A-loop); other site 1427342008200 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 1427342008201 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342008202 putative substrate translocation pore; other site 1427342008203 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 1427342008204 nucleoside/Zn binding site; other site 1427342008205 dimer interface [polypeptide binding]; other site 1427342008206 catalytic motif [active] 1427342008207 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1427342008208 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1427342008209 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1427342008210 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1427342008211 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008212 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342008213 dimerization interface [polypeptide binding]; other site 1427342008214 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DinB; COG2318 1427342008215 DinB superfamily; Region: DinB_2; pfam12867 1427342008216 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342008217 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 1427342008218 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342008219 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342008220 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342008221 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008222 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008223 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_2; cd08464 1427342008224 putative substrate binding pocket [chemical binding]; other site 1427342008225 putative dimerization interface [polypeptide binding]; other site 1427342008226 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR2; cd08268 1427342008227 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 1427342008228 putative NAD(P) binding site [chemical binding]; other site 1427342008229 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 1427342008230 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342008231 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342008232 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342008233 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008234 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342008235 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342008236 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 1427342008237 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 1427342008238 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 1427342008239 Cytochrome c553 [Energy production and conversion]; Region: COG2863 1427342008240 Cytochrome c; Region: Cytochrom_C; cl11414 1427342008241 Cytochrome c [Energy production and conversion]; Region: COG3258 1427342008242 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342008243 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342008244 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342008245 dimer interface [polypeptide binding]; other site 1427342008246 phosphorylation site [posttranslational modification] 1427342008247 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342008248 ATP binding site [chemical binding]; other site 1427342008249 G-X-G motif; other site 1427342008250 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 1427342008251 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342008252 active site 1427342008253 phosphorylation site [posttranslational modification] 1427342008254 intermolecular recognition site; other site 1427342008255 dimerization interface [polypeptide binding]; other site 1427342008256 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342008257 DNA binding site [nucleotide binding] 1427342008258 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 1427342008259 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 1427342008260 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 1427342008261 DsbD alpha interface [polypeptide binding]; other site 1427342008262 catalytic residues [active] 1427342008263 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 1427342008264 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 1427342008265 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342008266 catalytic residues [active] 1427342008267 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 1427342008268 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 1427342008269 dimerization domain [polypeptide binding]; other site 1427342008270 dimer interface [polypeptide binding]; other site 1427342008271 catalytic residues [active] 1427342008272 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 1427342008273 Cytochrome P450; Region: p450; cl12078 1427342008274 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 1427342008275 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 1427342008276 maleylacetoacetate isomerase; Region: maiA; TIGR01262 1427342008277 C-terminal domain interface [polypeptide binding]; other site 1427342008278 GSH binding site (G-site) [chemical binding]; other site 1427342008279 putative dimer interface [polypeptide binding]; other site 1427342008280 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 1427342008281 dimer interface [polypeptide binding]; other site 1427342008282 N-terminal domain interface [polypeptide binding]; other site 1427342008283 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 1427342008284 benzoate transport; Region: 2A0115; TIGR00895 1427342008285 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342008286 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342008287 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 1427342008288 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1427342008289 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3435 1427342008290 Cupin domain; Region: Cupin_2; pfam07883 1427342008291 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008292 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 1427342008293 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342008294 dimerization interface [polypeptide binding]; other site 1427342008295 RNA polymerase sigma factor; Provisional; Region: PRK12528 1427342008296 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342008297 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342008298 DNA binding residues [nucleotide binding] 1427342008299 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342008300 FecR protein; Region: FecR; pfam04773 1427342008301 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342008302 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 1427342008303 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342008304 N-terminal plug; other site 1427342008305 ligand-binding site [chemical binding]; other site 1427342008306 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342008307 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342008308 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 1427342008309 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 1427342008310 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 1427342008311 haemagglutination activity domain; Region: Haemagg_act; pfam05860 1427342008312 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342008313 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342008314 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 1427342008315 Bacterial EndoU nuclease; Region: EndoU_bacteria; pfam14436 1427342008316 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1427342008317 RHS Repeat; Region: RHS_repeat; pfam05593 1427342008318 RHS Repeat; Region: RHS_repeat; pfam05593 1427342008319 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1427342008320 RHS Repeat; Region: RHS_repeat; pfam05593 1427342008321 YD repeat (two copies); Region: YD_repeat_2x; TIGR01643 1427342008322 RHS Repeat; Region: RHS_repeat; pfam05593 1427342008323 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 1427342008324 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1427342008325 RHS Repeat; Region: RHS_repeat; pfam05593 1427342008326 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342008327 Coenzyme A binding pocket [chemical binding]; other site 1427342008328 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342008329 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342008330 S-adenosylmethionine binding site [chemical binding]; other site 1427342008331 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 1427342008332 Domain of unknown function (DUF3327); Region: DUF3327; pfam11806 1427342008333 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 1427342008334 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 1427342008335 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 1427342008336 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 1427342008337 putative aromatic amino acid binding site; other site 1427342008338 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342008339 Walker A motif; other site 1427342008340 ATP binding site [chemical binding]; other site 1427342008341 Walker B motif; other site 1427342008342 arginine finger; other site 1427342008343 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 1427342008344 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 1427342008345 active site 1427342008346 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 1427342008347 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008348 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008349 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342008350 dimerization interface [polypeptide binding]; other site 1427342008351 putative effector binding pocket; other site 1427342008352 glycine cleavage system protein H; Provisional; Region: PRK13380 1427342008353 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 1427342008354 lipoyl attachment site [posttranslational modification]; other site 1427342008355 glycine dehydrogenase; Provisional; Region: PRK05367 1427342008356 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 1427342008357 tetramer interface [polypeptide binding]; other site 1427342008358 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342008359 catalytic residue [active] 1427342008360 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 1427342008361 tetramer interface [polypeptide binding]; other site 1427342008362 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342008363 catalytic residue [active] 1427342008364 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1427342008365 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 1427342008366 dimer interface [polypeptide binding]; other site 1427342008367 active site 1427342008368 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1427342008369 folate binding site [chemical binding]; other site 1427342008370 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 1427342008371 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 1427342008372 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 1427342008373 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 1427342008374 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1427342008375 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The...; Region: SANT; cl17250 1427342008376 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1427342008377 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 1427342008378 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 1427342008379 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 1427342008380 HflC protein; Region: hflC; TIGR01932 1427342008381 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1427342008382 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 1427342008383 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 1427342008384 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342008385 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008386 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008387 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342008388 putative effector binding pocket; other site 1427342008389 dimerization interface [polypeptide binding]; other site 1427342008390 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342008391 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342008392 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 1427342008393 multidrug resistance protein MdtN; Provisional; Region: PRK10476 1427342008394 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342008395 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342008396 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 1427342008397 extracytoplasmic-function sigma-70 factor; Validated; Region: PRK07037 1427342008398 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342008399 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342008400 DNA binding residues [nucleotide binding] 1427342008401 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 1427342008402 peptide synthase; Validated; Region: PRK05691 1427342008403 Fatty acyl-AMP ligase (FAAL); Region: FAAL; cd05931 1427342008404 acyl-activating enzyme (AAE) consensus motif; other site 1427342008405 active site 1427342008406 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008407 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008408 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008409 acyl-activating enzyme (AAE) consensus motif; other site 1427342008410 AMP binding site [chemical binding]; other site 1427342008411 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008412 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008413 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008414 acyl-activating enzyme (AAE) consensus motif; other site 1427342008415 AMP binding site [chemical binding]; other site 1427342008416 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008417 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 1427342008418 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008419 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008420 acyl-activating enzyme (AAE) consensus motif; other site 1427342008421 AMP binding site [chemical binding]; other site 1427342008422 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008423 Prophage antirepressor [Transcription]; Region: COG3617 1427342008424 BRO family, N-terminal domain; Region: Bro-N; smart01040 1427342008425 HTH-like domain; Region: HTH_21; pfam13276 1427342008426 Integrase core domain; Region: rve; pfam00665 1427342008427 DDE domain; Region: DDE_Tnp_IS240; pfam13610 1427342008428 Integrase core domain; Region: rve_3; pfam13683 1427342008429 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 1427342008430 Transposase; Region: HTH_Tnp_1; pfam01527 1427342008431 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 1427342008432 CRISPR/Cas system-associated RAMP superfamily protein Csy3; Region: Csy3_I-F; cd09737 1427342008433 CRISPR/Cas system-associated RAMP superfamily protein Csy2; Region: Csy2_I-F; cd09736 1427342008434 CRISPR/Cas system-associated protein Csy1; Region: Csy1_I-F; cd09735 1427342008435 CRISPR/Cas system-associated protein Cas3/Cas2; Region: Cas3_Cas2_I-F; cd09673 1427342008436 CRISPR-associated helicase Cas3, subtype I-F/YPEST; Region: cas3_yersinia; TIGR02562 1427342008437 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 1427342008438 Transposase; Region: HTH_Tnp_1; pfam01527 1427342008439 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342008440 HTH-like domain; Region: HTH_21; pfam13276 1427342008441 Integrase core domain; Region: rve; pfam00665 1427342008442 Integrase core domain; Region: rve_3; pfam13683 1427342008443 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 1427342008444 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342008445 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342008446 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1427342008447 catalytic triad [active] 1427342008448 dimer interface [polypeptide binding]; other site 1427342008449 conserved cis-peptide bond; other site 1427342008450 Pirin-related protein [General function prediction only]; Region: COG1741 1427342008451 Pirin; Region: Pirin; pfam02678 1427342008452 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1427342008453 LysR family transcriptional regulator; Provisional; Region: PRK14997 1427342008454 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008455 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 1427342008456 putative effector binding pocket; other site 1427342008457 putative dimerization interface [polypeptide binding]; other site 1427342008458 trehalase; Provisional; Region: treA; PRK13272 1427342008459 Neutral trehalase [Carbohydrate transport and metabolism]; Region: TreA; COG1626 1427342008460 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 1427342008461 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 1427342008462 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06938 1427342008463 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342008464 inhibitor-cofactor binding pocket; inhibition site 1427342008465 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342008466 catalytic residue [active] 1427342008467 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3251 1427342008468 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 1427342008469 Serine hydrolase; Region: Ser_hydrolase; cl17834 1427342008470 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1427342008471 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1427342008472 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1427342008473 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 1427342008474 ABC-ATPase subunit interface; other site 1427342008475 dimer interface [polypeptide binding]; other site 1427342008476 putative PBP binding regions; other site 1427342008477 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1427342008478 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342008479 Walker A/P-loop; other site 1427342008480 ATP binding site [chemical binding]; other site 1427342008481 Q-loop/lid; other site 1427342008482 ABC transporter signature motif; other site 1427342008483 Walker B; other site 1427342008484 D-loop; other site 1427342008485 H-loop/switch region; other site 1427342008486 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1427342008487 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1427342008488 intersubunit interface [polypeptide binding]; other site 1427342008489 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342008490 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 1427342008491 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1427342008492 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342008493 peptide synthase; Provisional; Region: PRK12316 1427342008494 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008495 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008496 acyl-activating enzyme (AAE) consensus motif; other site 1427342008497 AMP binding site [chemical binding]; other site 1427342008498 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008499 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 1427342008500 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008501 acyl-activating enzyme (AAE) consensus motif; other site 1427342008502 AMP binding site [chemical binding]; other site 1427342008503 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008504 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008505 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008506 acyl-activating enzyme (AAE) consensus motif; other site 1427342008507 AMP binding site [chemical binding]; other site 1427342008508 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008509 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 1427342008510 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008511 acyl-activating enzyme (AAE) consensus motif; other site 1427342008512 AMP binding site [chemical binding]; other site 1427342008513 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008514 Condensation domain; Region: Condensation; pfam00668 1427342008515 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008516 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008517 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008518 acyl-activating enzyme (AAE) consensus motif; other site 1427342008519 AMP binding site [chemical binding]; other site 1427342008520 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008521 Condensation domain; Region: Condensation; pfam00668 1427342008522 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008523 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008524 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008525 acyl-activating enzyme (AAE) consensus motif; other site 1427342008526 AMP binding site [chemical binding]; other site 1427342008527 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008528 Condensation domain; Region: Condensation; pfam00668 1427342008529 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008530 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008531 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008532 acyl-activating enzyme (AAE) consensus motif; other site 1427342008533 AMP binding site [chemical binding]; other site 1427342008534 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008535 Condensation domain; Region: Condensation; pfam00668 1427342008536 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008537 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008538 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008539 acyl-activating enzyme (AAE) consensus motif; other site 1427342008540 AMP binding site [chemical binding]; other site 1427342008541 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008542 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3319 1427342008543 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342008544 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 1427342008545 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342008546 N-terminal plug; other site 1427342008547 ligand-binding site [chemical binding]; other site 1427342008548 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 1427342008549 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342008550 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342008551 Walker A/P-loop; other site 1427342008552 ATP binding site [chemical binding]; other site 1427342008553 Q-loop/lid; other site 1427342008554 ABC transporter signature motif; other site 1427342008555 Walker B; other site 1427342008556 D-loop; other site 1427342008557 H-loop/switch region; other site 1427342008558 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1427342008559 catalytic site [active] 1427342008560 Uncharacterized conserved protein [Function unknown]; Region: COG1262 1427342008561 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 1427342008562 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1427342008563 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342008564 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342008565 catalytic residue [active] 1427342008566 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 1427342008567 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 1427342008568 active site 1427342008569 dimer interface [polypeptide binding]; other site 1427342008570 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342008571 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 1427342008572 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342008573 Walker A/P-loop; other site 1427342008574 ATP binding site [chemical binding]; other site 1427342008575 Q-loop/lid; other site 1427342008576 ABC transporter signature motif; other site 1427342008577 Walker B; other site 1427342008578 D-loop; other site 1427342008579 H-loop/switch region; other site 1427342008580 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1427342008581 FtsX-like permease family; Region: FtsX; pfam02687 1427342008582 macrolide transporter subunit MacA; Provisional; Region: PRK11578 1427342008583 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342008584 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342008585 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342008586 FecR protein; Region: FecR; pfam04773 1427342008587 RNA polymerase sigma factor; Reviewed; Region: PRK12527 1427342008588 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342008589 DNA binding residues [nucleotide binding] 1427342008590 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 1427342008591 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342008592 Penicillin amidase; Region: Penicil_amidase; pfam01804 1427342008593 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 1427342008594 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 1427342008595 active site 1427342008596 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 1427342008597 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 1427342008598 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342008599 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008600 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342008601 dimerization interface [polypeptide binding]; other site 1427342008602 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 1427342008603 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 1427342008604 phosphate binding site [ion binding]; other site 1427342008605 Protein of unknown function (DUF1654); Region: DUF1654; pfam07867 1427342008606 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1427342008607 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342008608 catalytic loop [active] 1427342008609 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 1427342008610 iron binding site [ion binding]; other site 1427342008611 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342008612 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342008613 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342008614 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1427342008615 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342008616 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342008617 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342008618 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342008619 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342008620 active site 1427342008621 phosphorylation site [posttranslational modification] 1427342008622 intermolecular recognition site; other site 1427342008623 dimerization interface [polypeptide binding]; other site 1427342008624 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342008625 DNA binding residues [nucleotide binding] 1427342008626 dimerization interface [polypeptide binding]; other site 1427342008627 Domain of unknown function (DUF4280); Region: DUF4280; pfam14107 1427342008628 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 1427342008629 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342008630 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342008631 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342008632 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 1427342008633 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 1427342008634 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342008635 Walker A motif; other site 1427342008636 ATP binding site [chemical binding]; other site 1427342008637 Walker B motif; other site 1427342008638 arginine finger; other site 1427342008639 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342008640 Walker A motif; other site 1427342008641 ATP binding site [chemical binding]; other site 1427342008642 Walker B motif; other site 1427342008643 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3520 1427342008644 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 1427342008645 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 1427342008646 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3518 1427342008647 Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport]; Region: Hcp; COG3157 1427342008648 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 1427342008649 Protein of unknown function (DUF877); Region: DUF877; pfam05943 1427342008650 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3516 1427342008651 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 1427342008652 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 1427342008653 Type VI protein secretion system component VasF [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3455 1427342008654 Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]; Region: IcmF; COG3523 1427342008655 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 1427342008656 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 1427342008657 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1427342008658 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342008659 Walker A motif; other site 1427342008660 ATP binding site [chemical binding]; other site 1427342008661 Walker B motif; other site 1427342008662 arginine finger; other site 1427342008663 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1427342008664 FMN reductase, MsuE subfamily; Region: FMN_reduc_MsuE; TIGR03566 1427342008665 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342008666 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 1427342008667 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342008668 active site 1427342008669 dimer interface [polypeptide binding]; other site 1427342008670 non-prolyl cis peptide bond; other site 1427342008671 insertion regions; other site 1427342008672 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 1427342008673 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 1427342008674 Flavin binding site [chemical binding]; other site 1427342008675 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1427342008676 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342008677 Walker A motif; other site 1427342008678 ATP binding site [chemical binding]; other site 1427342008679 Walker B motif; other site 1427342008680 arginine finger; other site 1427342008681 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1427342008682 Predicted ATPase [General function prediction only]; Region: COG1485 1427342008683 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342008684 Walker B; other site 1427342008685 D-loop; other site 1427342008686 H-loop/switch region; other site 1427342008687 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 1427342008688 Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins; Region: GDPD_SaGlpQ_like; cd08601 1427342008689 active site 1427342008690 catalytic site [active] 1427342008691 metal binding site [ion binding]; metal-binding site 1427342008692 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342008693 dimer interface [polypeptide binding]; other site 1427342008694 conserved gate region; other site 1427342008695 ABC-ATPase subunit interface; other site 1427342008696 ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]; Region: AbcC; COG1135 1427342008697 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 1427342008698 Walker A/P-loop; other site 1427342008699 ATP binding site [chemical binding]; other site 1427342008700 Q-loop/lid; other site 1427342008701 ABC transporter signature motif; other site 1427342008702 Walker B; other site 1427342008703 D-loop; other site 1427342008704 H-loop/switch region; other site 1427342008705 NIL domain; Region: NIL; pfam09383 1427342008706 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1427342008707 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1427342008708 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 1427342008709 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 1427342008710 active site 1427342008711 non-prolyl cis peptide bond; other site 1427342008712 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 1427342008713 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342008714 active site 1427342008715 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 1427342008716 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342008717 active site 1427342008718 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342008719 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 1427342008720 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1427342008721 putative substrate binding site [chemical binding]; other site 1427342008722 putative ATP binding site [chemical binding]; other site 1427342008723 D-xylulose kinases, subgroup 1; members of the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_1; cd07809 1427342008724 N- and C-terminal domain interface [polypeptide binding]; other site 1427342008725 D-xylulose kinase; Region: XylB; TIGR01312 1427342008726 active site 1427342008727 MgATP binding site [chemical binding]; other site 1427342008728 catalytic site [active] 1427342008729 metal binding site [ion binding]; metal-binding site 1427342008730 xylulose binding site [chemical binding]; other site 1427342008731 putative homodimer interface [polypeptide binding]; other site 1427342008732 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 1427342008733 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 1427342008734 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 1427342008735 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 1427342008736 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 1427342008737 Walker A/P-loop; other site 1427342008738 ATP binding site [chemical binding]; other site 1427342008739 Q-loop/lid; other site 1427342008740 ABC transporter signature motif; other site 1427342008741 Walker B; other site 1427342008742 D-loop; other site 1427342008743 H-loop/switch region; other site 1427342008744 TOBE domain; Region: TOBE_2; pfam08402 1427342008745 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 1427342008746 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342008747 dimer interface [polypeptide binding]; other site 1427342008748 conserved gate region; other site 1427342008749 ABC-ATPase subunit interface; other site 1427342008750 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342008751 dimer interface [polypeptide binding]; other site 1427342008752 conserved gate region; other site 1427342008753 putative PBP binding loops; other site 1427342008754 ABC-ATPase subunit interface; other site 1427342008755 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 1427342008756 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1427342008757 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342008758 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342008759 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008760 Arylsulfotransferase (ASST); Region: Arylsulfotrans; pfam05935 1427342008761 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1427342008762 substrate binding site [chemical binding]; other site 1427342008763 activation loop (A-loop); other site 1427342008764 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342008765 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342008766 N-terminal plug; other site 1427342008767 ligand-binding site [chemical binding]; other site 1427342008768 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008769 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008770 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342008771 dimerization interface [polypeptide binding]; other site 1427342008772 Sulfatase; Region: Sulfatase; cl17466 1427342008773 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 1427342008774 Cupin; Region: Cupin_6; pfam12852 1427342008775 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342008776 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008777 Uncharacterized conserved protein [Function unknown]; Region: COG2128 1427342008778 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 1427342008779 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342008780 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342008781 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1427342008782 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342008783 Walker A/P-loop; other site 1427342008784 ATP binding site [chemical binding]; other site 1427342008785 Q-loop/lid; other site 1427342008786 ABC transporter signature motif; other site 1427342008787 Walker B; other site 1427342008788 D-loop; other site 1427342008789 H-loop/switch region; other site 1427342008790 NMT1-like family; Region: NMT1_2; pfam13379 1427342008791 NMT1/THI5 like; Region: NMT1; pfam09084 1427342008792 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342008793 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342008794 dimer interface [polypeptide binding]; other site 1427342008795 conserved gate region; other site 1427342008796 putative PBP binding loops; other site 1427342008797 ABC-ATPase subunit interface; other site 1427342008798 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 1427342008799 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 1427342008800 active site 1427342008801 non-prolyl cis peptide bond; other site 1427342008802 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 1427342008803 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 1427342008804 Flavin binding site [chemical binding]; other site 1427342008805 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 1427342008806 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 1427342008807 Flavin binding site [chemical binding]; other site 1427342008808 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 1427342008809 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1427342008810 tetrameric interface [polypeptide binding]; other site 1427342008811 activator binding site; other site 1427342008812 NADP binding site [chemical binding]; other site 1427342008813 substrate binding site [chemical binding]; other site 1427342008814 catalytic residues [active] 1427342008815 GntP family permease; Region: GntP_permease; pfam02447 1427342008816 fructuronate transporter; Provisional; Region: PRK10034; cl15264 1427342008817 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 1427342008818 AAA domain; Region: AAA_33; pfam13671 1427342008819 ATP-binding site [chemical binding]; other site 1427342008820 Gluconate-6-phosphate binding site [chemical binding]; other site 1427342008821 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1427342008822 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1427342008823 DNA binding site [nucleotide binding] 1427342008824 domain linker motif; other site 1427342008825 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 1427342008826 putative ligand binding site [chemical binding]; other site 1427342008827 putative dimerization interface [polypeptide binding]; other site 1427342008828 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 1427342008829 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342008830 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342008831 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008832 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008833 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_7; cd08476 1427342008834 putative dimerization interface [polypeptide binding]; other site 1427342008835 putative effector binding pocket; other site 1427342008836 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342008837 Beta-lactamase; Region: Beta-lactamase; pfam00144 1427342008838 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342008839 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342008840 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1427342008841 non-specific DNA binding site [nucleotide binding]; other site 1427342008842 salt bridge; other site 1427342008843 sequence-specific DNA binding site [nucleotide binding]; other site 1427342008844 Cupin domain; Region: Cupin_2; pfam07883 1427342008845 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342008846 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 1427342008847 active site 1427342008848 iron coordination sites [ion binding]; other site 1427342008849 substrate binding pocket [chemical binding]; other site 1427342008850 NMT1-like family; Region: NMT1_2; pfam13379 1427342008851 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 1427342008852 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1427342008853 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342008854 Walker A/P-loop; other site 1427342008855 ATP binding site [chemical binding]; other site 1427342008856 Q-loop/lid; other site 1427342008857 ABC transporter signature motif; other site 1427342008858 Walker B; other site 1427342008859 D-loop; other site 1427342008860 H-loop/switch region; other site 1427342008861 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342008862 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342008863 putative PBP binding loops; other site 1427342008864 ABC-ATPase subunit interface; other site 1427342008865 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342008866 The adenylation domain of nonribosomal peptide synthetases (NRPS), including Saframycin A gene cluster from Streptomyces lavendulae; Region: A_NRPS_Sfm_like; cd12115 1427342008867 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 1427342008868 acyl-activating enzyme (AAE) consensus motif; other site 1427342008869 AMP binding site [chemical binding]; other site 1427342008870 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008871 Condensation domain; Region: Condensation; pfam00668 1427342008872 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008873 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 1427342008874 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 1427342008875 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 1427342008876 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 1427342008877 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 1427342008878 acyl-activating enzyme (AAE) consensus motif; other site 1427342008879 AMP binding site [chemical binding]; other site 1427342008880 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 1427342008881 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1427342008882 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 1427342008883 Condensation domain; Region: Condensation; pfam00668 1427342008884 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 1427342008885 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 1427342008886 PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's...; Region: PA2301; cd04939 1427342008887 putative deacylase active site [active] 1427342008888 GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18; Region: GH18_chitinase_D-like; cd02871 1427342008889 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 1427342008890 putative active site [active] 1427342008891 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 1427342008892 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 1427342008893 Interdomain contacts; other site 1427342008894 Cytokine receptor motif; other site 1427342008895 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 1427342008896 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 1427342008897 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342008898 DNA-binding site [nucleotide binding]; DNA binding site 1427342008899 UTRA domain; Region: UTRA; pfam07702 1427342008900 putative oxidoreductase; Provisional; Region: PRK08275 1427342008901 L-aspartate oxidase; Provisional; Region: PRK06175 1427342008902 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1427342008903 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1427342008904 taurine ABC transporter, periplasmic binding protein; Region: taurine_ABC_bnd; TIGR01729 1427342008905 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342008906 substrate binding pocket [chemical binding]; other site 1427342008907 membrane-bound complex binding site; other site 1427342008908 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1427342008909 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 1427342008910 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1427342008911 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1427342008912 Walker A/P-loop; other site 1427342008913 ATP binding site [chemical binding]; other site 1427342008914 Q-loop/lid; other site 1427342008915 ABC transporter signature motif; other site 1427342008916 Walker B; other site 1427342008917 D-loop; other site 1427342008918 H-loop/switch region; other site 1427342008919 HEAT repeats; Region: HEAT_2; pfam13646 1427342008920 HEAT repeats; Region: HEAT_2; pfam13646 1427342008921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 1427342008922 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 1427342008923 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 1427342008924 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 1427342008925 Trp docking motif [polypeptide binding]; other site 1427342008926 putative active site [active] 1427342008927 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342008928 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342008929 N-terminal plug; other site 1427342008930 ligand-binding site [chemical binding]; other site 1427342008931 Peptidase family M48; Region: Peptidase_M48; cl12018 1427342008932 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 1427342008933 Peptidase family M48; Region: Peptidase_M48; cl12018 1427342008934 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342008935 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008936 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1427342008937 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342008938 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1427342008939 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1427342008940 active site 1427342008941 arsenical pump membrane protein; Provisional; Region: PRK15445 1427342008942 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 1427342008943 transmembrane helices; other site 1427342008944 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342008945 dimerization interface [polypeptide binding]; other site 1427342008946 putative DNA binding site [nucleotide binding]; other site 1427342008947 putative Zn2+ binding site [ion binding]; other site 1427342008948 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 1427342008949 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342008950 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342008951 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1427342008952 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 1427342008953 putative NAD(P) binding site [chemical binding]; other site 1427342008954 putative substrate binding site [chemical binding]; other site 1427342008955 catalytic Zn binding site [ion binding]; other site 1427342008956 structural Zn binding site [ion binding]; other site 1427342008957 dimer interface [polypeptide binding]; other site 1427342008958 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 1427342008959 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 1427342008960 DNA binding residues [nucleotide binding] 1427342008961 dimer interface [polypeptide binding]; other site 1427342008962 [2Fe-2S] cluster binding site [ion binding]; other site 1427342008963 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1427342008964 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1427342008965 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1427342008966 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342008967 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342008968 Coenzyme A binding pocket [chemical binding]; other site 1427342008969 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342008970 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342008971 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342008972 CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]; Region: PyrG; COG0504 1427342008973 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1427342008974 active site 1427342008975 putative oxyanion hole; other site 1427342008976 catalytic triad [active] 1427342008977 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 1427342008978 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342008979 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342008980 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342008981 dimerization interface [polypeptide binding]; other site 1427342008982 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342008983 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342008984 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342008985 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 1427342008986 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342008987 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 1427342008988 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 1427342008989 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 1427342008990 dimerization interface [polypeptide binding]; other site 1427342008991 ligand binding site [chemical binding]; other site 1427342008992 NADP binding site [chemical binding]; other site 1427342008993 catalytic site [active] 1427342008994 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342008995 D-galactonate transporter; Region: 2A0114; TIGR00893 1427342008996 putative substrate translocation pore; other site 1427342008997 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 1427342008998 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1427342008999 substrate binding site [chemical binding]; other site 1427342009000 ATP binding site [chemical binding]; other site 1427342009001 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 1427342009002 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1427342009003 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1427342009004 DNA binding site [nucleotide binding] 1427342009005 domain linker motif; other site 1427342009006 Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Region: PBP1_RegR_EndR_KdgR_like; cd06283 1427342009007 putative dimerization interface [polypeptide binding]; other site 1427342009008 putative ligand binding site [chemical binding]; other site 1427342009009 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009010 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009011 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342009012 putative effector binding pocket; other site 1427342009013 dimerization interface [polypeptide binding]; other site 1427342009014 Cytochrome c553 [Energy production and conversion]; Region: COG2863 1427342009015 Cytochrome c; Region: Cytochrom_C; cl11414 1427342009016 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2368 1427342009017 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 1427342009018 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 1427342009019 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cd00250 1427342009020 substrate binding pocket [chemical binding]; other site 1427342009021 active site 1427342009022 iron coordination sites [ion binding]; other site 1427342009023 Pyoverdine/dityrosine biosynthesis protein [Secondary metabolites biosynthesis, transport, and catabolism]; Region: DIT1; COG3207 1427342009024 Pyoverdine/dityrosine biosynthesis protein; Region: DIT1_PvcA; pfam05141 1427342009025 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 1427342009026 active site 1427342009027 homodimer interface [polypeptide binding]; other site 1427342009028 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1427342009029 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1427342009030 Helix-turn-helix domain; Region: HTH_19; pfam12844 1427342009031 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 1427342009032 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342009033 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1427342009034 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 1427342009035 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342009036 E3 interaction surface; other site 1427342009037 lipoyl attachment site [posttranslational modification]; other site 1427342009038 e3 binding domain; Region: E3_binding; pfam02817 1427342009039 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1427342009040 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 1427342009041 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 1427342009042 alpha subunit interface [polypeptide binding]; other site 1427342009043 TPP binding site [chemical binding]; other site 1427342009044 heterodimer interface [polypeptide binding]; other site 1427342009045 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1427342009046 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 1427342009047 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 1427342009048 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 1427342009049 tetramer interface [polypeptide binding]; other site 1427342009050 TPP-binding site [chemical binding]; other site 1427342009051 heterodimer interface [polypeptide binding]; other site 1427342009052 phosphorylation loop region [posttranslational modification] 1427342009053 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342009054 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342009055 putative DNA binding site [nucleotide binding]; other site 1427342009056 putative Zn2+ binding site [ion binding]; other site 1427342009057 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342009058 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 1427342009059 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 1427342009060 active site 1427342009061 DNA binding site [nucleotide binding] 1427342009062 Int/Topo IB signature motif; other site 1427342009063 catalytic residues [active] 1427342009064 putative FAD-binding dehydrogenase; Reviewed; Region: PRK06134 1427342009065 Predicted oxidoreductase [General function prediction only]; Region: COG3573 1427342009066 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 1427342009067 Acyltransferase family; Region: Acyl_transf_3; pfam01757 1427342009068 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1427342009069 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 1427342009070 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342009071 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 1427342009072 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 1427342009073 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 1427342009074 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3664 1427342009075 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342009076 This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides; Region: GT1_ecORF704_like; cd03822 1427342009077 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 1427342009078 Chain length determinant protein; Region: Wzz; cl15801 1427342009079 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 1427342009080 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 1427342009081 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 1427342009082 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 1427342009083 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 1427342009084 active site 1427342009085 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1427342009086 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1427342009087 Substrate binding site; other site 1427342009088 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 1427342009089 CoA-binding domain; Region: CoA_binding_3; pfam13727 1427342009090 Bacterial sugar transferase; Region: Bac_transf; cl00939 1427342009091 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342009092 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342009093 catalytic residue [active] 1427342009094 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 1427342009095 MOSC domain; Region: MOSC; pfam03473 1427342009096 3-alpha domain; Region: 3-alpha; pfam03475 1427342009097 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 1427342009098 classical (c) SDRs; Region: SDR_c; cd05233 1427342009099 NAD(P) binding site [chemical binding]; other site 1427342009100 active site 1427342009101 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1427342009102 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1427342009103 Phage replication protein CRI; Region: Phage_CRI; pfam05144 1427342009104 Zonular occludens toxin (Zot); Region: Zot; cl17485 1427342009105 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 1427342009106 Zonular occludens toxin (Zot); Region: Zot; cl17485 1427342009107 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2508 1427342009108 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1427342009109 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 1427342009110 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 1427342009111 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 1427342009112 Outer membrane efflux protein; Region: OEP; pfam02321 1427342009113 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 1427342009114 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342009115 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 1427342009116 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1427342009117 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 1427342009118 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 1427342009119 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 1427342009120 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 1427342009121 Phage protein Gp37/Gp68; Region: Gp37_Gp68; pfam07505 1427342009122 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 1427342009123 DNA binding site [nucleotide binding] 1427342009124 dimer interface [polypeptide binding]; other site 1427342009125 active site 1427342009126 Int/Topo IB signature motif; other site 1427342009127 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 1427342009128 Transposase domain (DUF772); Region: DUF772; pfam05598 1427342009129 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 1427342009130 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 1427342009131 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 1427342009132 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 1427342009133 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 1427342009134 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342009135 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342009136 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 1427342009137 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342009138 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 1427342009139 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 1427342009140 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342009141 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1427342009142 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1427342009143 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 1427342009144 active site 1427342009145 NAD binding site [chemical binding]; other site 1427342009146 metal binding site [ion binding]; metal-binding site 1427342009147 amino acid transporter; Region: 2A0306; TIGR00909 1427342009148 gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK13473 1427342009149 Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like; Region: ALDH_ABALDH-YdcW; cd07092 1427342009150 tetrameric interface [polypeptide binding]; other site 1427342009151 NAD binding site [chemical binding]; other site 1427342009152 catalytic residues [active] 1427342009153 substrate binding site [chemical binding]; other site 1427342009154 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 1427342009155 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342009156 inhibitor-cofactor binding pocket; inhibition site 1427342009157 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342009158 catalytic residue [active] 1427342009159 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1427342009160 NAD binding domain of 6-phosphogluconate dehydrogenase; Region: NAD_binding_2; pfam03446 1427342009161 NAD binding site [chemical binding]; other site 1427342009162 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1427342009163 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 1427342009164 Na binding site [ion binding]; other site 1427342009165 Protein of unknown function, DUF485; Region: DUF485; pfam04341 1427342009166 acyl-CoA synthetase; Validated; Region: PRK08162 1427342009167 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 1427342009168 acyl-activating enzyme (AAE) consensus motif; other site 1427342009169 putative active site [active] 1427342009170 AMP binding site [chemical binding]; other site 1427342009171 putative CoA binding site [chemical binding]; other site 1427342009172 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342009173 classical (c) SDRs; Region: SDR_c; cd05233 1427342009174 NAD(P) binding site [chemical binding]; other site 1427342009175 active site 1427342009176 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342009177 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 1427342009178 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 1427342009179 active site 1427342009180 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342009181 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 1427342009182 putative active site [active] 1427342009183 putative substrate binding site [chemical binding]; other site 1427342009184 ATP binding site [chemical binding]; other site 1427342009185 Propionate catabolism activator; Region: PrpR_N; pfam06506 1427342009186 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342009187 PAS domain; Region: PAS_9; pfam13426 1427342009188 putative active site [active] 1427342009189 heme pocket [chemical binding]; other site 1427342009190 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1427342009191 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342009192 Walker A motif; other site 1427342009193 ATP binding site [chemical binding]; other site 1427342009194 Walker B motif; other site 1427342009195 arginine finger; other site 1427342009196 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342009197 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 1427342009198 mce related protein; Region: MCE; pfam02470 1427342009199 mce related protein; Region: MCE; pfam02470 1427342009200 mce related protein; Region: MCE; pfam02470 1427342009201 mce related protein; Region: MCE; pfam02470 1427342009202 mce related protein; Region: MCE; pfam02470 1427342009203 mce related protein; Region: MCE; pfam02470 1427342009204 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 1427342009205 Paraquat-inducible protein A; Region: PqiA; pfam04403 1427342009206 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1427342009207 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 1427342009208 dimer interface [polypeptide binding]; other site 1427342009209 NADP binding site [chemical binding]; other site 1427342009210 catalytic residues [active] 1427342009211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: GguC; COG3802 1427342009212 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1427342009213 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 1427342009214 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_2; cd03327 1427342009215 putative active site pocket [active] 1427342009216 putative metal binding site [ion binding]; other site 1427342009217 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 1427342009218 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009219 putative substrate translocation pore; other site 1427342009220 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342009221 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 1427342009222 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 1427342009223 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 1427342009224 Amidohydrolase; Region: Amidohydro_2; pfam04909 1427342009225 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009226 D-galactonate transporter; Region: 2A0114; TIGR00893 1427342009227 putative substrate translocation pore; other site 1427342009228 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 1427342009229 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 1427342009230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 1427342009231 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009232 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009233 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342009234 dimerization interface [polypeptide binding]; other site 1427342009235 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342009236 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342009237 substrate binding pocket [chemical binding]; other site 1427342009238 membrane-bound complex binding site; other site 1427342009239 hinge residues; other site 1427342009240 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342009241 dimer interface [polypeptide binding]; other site 1427342009242 conserved gate region; other site 1427342009243 putative PBP binding loops; other site 1427342009244 ABC-ATPase subunit interface; other site 1427342009245 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342009246 dimer interface [polypeptide binding]; other site 1427342009247 conserved gate region; other site 1427342009248 putative PBP binding loops; other site 1427342009249 ABC-ATPase subunit interface; other site 1427342009250 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 1427342009251 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 1427342009252 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 1427342009253 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342009254 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 1427342009255 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342009256 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 1427342009257 Prostaglandin dehydrogenases; Region: PGDH; cd05288 1427342009258 NAD(P) binding site [chemical binding]; other site 1427342009259 substrate binding site [chemical binding]; other site 1427342009260 dimer interface [polypeptide binding]; other site 1427342009261 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342009262 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342009263 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342009264 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342009265 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342009266 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342009267 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1427342009268 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342009269 catalytic loop [active] 1427342009270 iron binding site [ion binding]; other site 1427342009271 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 1427342009272 FOG: CBS domain [General function prediction only]; Region: COG0517 1427342009273 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 1427342009274 Anthrax toxin LF subunit; Region: Anthrax_toxA; pfam03497 1427342009275 General stress protein [General function prediction only]; Region: GsiB; COG3729 1427342009276 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1427342009277 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 1427342009278 active site 1427342009279 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 1427342009280 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342009281 NAD binding site [chemical binding]; other site 1427342009282 catalytic Zn binding site [ion binding]; other site 1427342009283 structural Zn binding site [ion binding]; other site 1427342009284 Low affinity iron permease; Region: Iron_permease; pfam04120 1427342009285 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 1427342009286 dimanganese center [ion binding]; other site 1427342009287 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3685 1427342009288 Predicted membrane protein [Function unknown]; Region: COG3205 1427342009289 carboxylate-amine ligase; Provisional; Region: PRK13515 1427342009290 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 1427342009291 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 1427342009292 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342009293 S-adenosylmethionine binding site [chemical binding]; other site 1427342009294 Yip1 domain; Region: Yip1; cl17815 1427342009295 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342009296 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342009297 putative active site [active] 1427342009298 heme pocket [chemical binding]; other site 1427342009299 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1427342009300 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342009301 putative active site [active] 1427342009302 heme pocket [chemical binding]; other site 1427342009303 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342009304 dimer interface [polypeptide binding]; other site 1427342009305 phosphorylation site [posttranslational modification] 1427342009306 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342009307 ATP binding site [chemical binding]; other site 1427342009308 Mg2+ binding site [ion binding]; other site 1427342009309 G-X-G motif; other site 1427342009310 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342009311 active site 1427342009312 phosphorylation site [posttranslational modification] 1427342009313 intermolecular recognition site; other site 1427342009314 dimerization interface [polypeptide binding]; other site 1427342009315 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 1427342009316 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1427342009317 metal binding site [ion binding]; metal-binding site 1427342009318 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 1427342009319 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 1427342009320 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 1427342009321 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342009322 Protein of unknown function (DUF3182); Region: DUF3182; pfam11379 1427342009323 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 1427342009324 glycogen synthase; Provisional; Region: glgA; PRK00654 1427342009325 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 1427342009326 ADP-binding pocket [chemical binding]; other site 1427342009327 homodimer interface [polypeptide binding]; other site 1427342009328 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 1427342009329 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 1427342009330 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 1427342009331 catalytic site [active] 1427342009332 active site 1427342009333 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 1427342009334 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 1427342009335 Maltooligosyl trehalose synthase [Carbohydrate transport and metabolism]; Region: TreY; COG3280 1427342009336 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 1427342009337 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 1427342009338 active site 1427342009339 catalytic site [active] 1427342009340 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 1427342009341 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 1427342009342 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 1427342009343 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 1427342009344 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 1427342009345 active site 1427342009346 catalytic site [active] 1427342009347 FOG: CBS domain [General function prediction only]; Region: COG0517 1427342009348 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 1427342009349 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 1427342009350 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342009351 NAD binding site [chemical binding]; other site 1427342009352 catalytic Zn binding site [ion binding]; other site 1427342009353 structural Zn binding site [ion binding]; other site 1427342009354 Protein of unknown function DUF72; Region: DUF72; pfam01904 1427342009355 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 1427342009356 putative catalytic site [active] 1427342009357 putative metal binding site [ion binding]; other site 1427342009358 putative phosphate binding site [ion binding]; other site 1427342009359 cardiolipin synthase 2; Provisional; Region: PRK11263 1427342009360 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 1427342009361 putative active site [active] 1427342009362 catalytic site [active] 1427342009363 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1427342009364 putative active site [active] 1427342009365 catalytic site [active] 1427342009366 Predicted integral membrane protein [Function unknown]; Region: COG0392 1427342009367 glycogen branching enzyme; Provisional; Region: PRK05402 1427342009368 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 1427342009369 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 1427342009370 active site 1427342009371 catalytic site [active] 1427342009372 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 1427342009373 trehalose synthase; Region: treS_nterm; TIGR02456 1427342009374 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 1427342009375 active site 1427342009376 catalytic site [active] 1427342009377 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 1427342009378 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 1427342009379 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 1427342009380 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 1427342009381 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 1427342009382 active site 1427342009383 homodimer interface [polypeptide binding]; other site 1427342009384 catalytic site [active] 1427342009385 acceptor binding site [chemical binding]; other site 1427342009386 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 1427342009387 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 1427342009388 putative DNA binding site [nucleotide binding]; other site 1427342009389 putative homodimer interface [polypeptide binding]; other site 1427342009390 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 1427342009391 MgtC family; Region: MgtC; pfam02308 1427342009392 hydroperoxidase II; Provisional; Region: katE; PRK11249 1427342009393 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 1427342009394 tetramer interface [polypeptide binding]; other site 1427342009395 heme binding pocket [chemical binding]; other site 1427342009396 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 1427342009397 domain interactions; other site 1427342009398 General stress protein [General function prediction only]; Region: GsiB; COG3729 1427342009399 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 1427342009400 homodimer interface [polypeptide binding]; other site 1427342009401 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 1427342009402 active site pocket [active] 1427342009403 Hypothetical protein (DUF2513); Region: DUF2513; pfam10711 1427342009404 short chain dehydrogenase; Provisional; Region: PRK06701 1427342009405 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 1427342009406 NAD binding site [chemical binding]; other site 1427342009407 metal binding site [ion binding]; metal-binding site 1427342009408 active site 1427342009409 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 1427342009410 Prokaryotic metallothionein; Region: Metallothio_Pro; pfam02069 1427342009411 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 1427342009412 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 1427342009413 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 1427342009414 active site 1427342009415 DNA binding site [nucleotide binding] 1427342009416 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 1427342009417 DNA binding site [nucleotide binding] 1427342009418 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 1427342009419 nucleotide binding site [chemical binding]; other site 1427342009420 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342009421 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 1427342009422 active site 1427342009423 phosphorylation site [posttranslational modification] 1427342009424 intermolecular recognition site; other site 1427342009425 dimerization interface [polypeptide binding]; other site 1427342009426 Predicted membrane protein [Function unknown]; Region: COG2323 1427342009427 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1427342009428 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1427342009429 Predicted outer membrane protein [Function unknown]; Region: COG3652 1427342009430 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342009431 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1427342009432 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342009433 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 1427342009434 Fimbrial protein; Region: Fimbrial; cl01416 1427342009435 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 1427342009436 PapC N-terminal domain; Region: PapC_N; pfam13954 1427342009437 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 1427342009438 PapC C-terminal domain; Region: PapC_C; pfam13953 1427342009439 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1427342009440 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342009441 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 1427342009442 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 1427342009443 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 1427342009444 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 1427342009445 Active Sites [active] 1427342009446 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 1427342009447 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1427342009448 ParB-like nuclease domain; Region: ParBc; pfam02195 1427342009449 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342009450 Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like; Region: ALDH_PsfA-ACA09737; cd07120 1427342009451 NAD(P) binding site [chemical binding]; other site 1427342009452 catalytic residues [active] 1427342009453 choline dehydrogenase; Validated; Region: PRK02106 1427342009454 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342009455 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342009456 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009457 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009458 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342009459 putative effector binding pocket; other site 1427342009460 dimerization interface [polypeptide binding]; other site 1427342009461 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cd07812 1427342009462 hydrophobic ligand binding site; other site 1427342009463 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 1427342009464 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009465 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 1427342009466 substrate binding pocket [chemical binding]; other site 1427342009467 dimerization interface [polypeptide binding]; other site 1427342009468 SnoaL-like domain; Region: SnoaL_2; pfam12680 1427342009469 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1427342009470 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 1427342009471 tetramer interface [polypeptide binding]; other site 1427342009472 catalytic Zn binding site [ion binding]; other site 1427342009473 NADP binding site [chemical binding]; other site 1427342009474 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342009475 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 1427342009476 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1427342009477 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342009478 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 1427342009479 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1427342009480 DNA binding site [nucleotide binding] 1427342009481 active site 1427342009482 Uncharacterized conserved protein [Function unknown]; Region: COG4336 1427342009483 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009484 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009485 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342009486 dimerization interface [polypeptide binding]; other site 1427342009487 benzoate transport; Region: 2A0115; TIGR00895 1427342009488 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009489 putative substrate translocation pore; other site 1427342009490 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342009491 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 1427342009492 putative active site [active] 1427342009493 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 1427342009494 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1427342009495 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 1427342009496 Predicted outer membrane protein [Function unknown]; Region: COG3652 1427342009497 thiamine pyrophosphate protein; Provisional; Region: PRK08273 1427342009498 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 1427342009499 PYR/PP interface [polypeptide binding]; other site 1427342009500 dimer interface [polypeptide binding]; other site 1427342009501 tetramer interface [polypeptide binding]; other site 1427342009502 TPP binding site [chemical binding]; other site 1427342009503 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342009504 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 1427342009505 TPP-binding site [chemical binding]; other site 1427342009506 short chain dehydrogenase; Provisional; Region: PRK08267 1427342009507 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342009508 NAD(P) binding site [chemical binding]; other site 1427342009509 active site 1427342009510 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 1427342009511 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 1427342009512 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 1427342009513 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342009514 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342009515 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342009516 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342009517 FecR protein; Region: FecR; pfam04773 1427342009518 RNA polymerase sigma factor; Provisional; Region: PRK12525 1427342009519 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342009520 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342009521 DNA binding residues [nucleotide binding] 1427342009522 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342009523 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 1427342009524 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342009525 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009526 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 1427342009527 probable F420-dependent oxidoreductase, Rv3520c family; Region: F420_Rv3520c; TIGR03559 1427342009528 dimer interface [polypeptide binding]; other site 1427342009529 active site 1427342009530 non-prolyl cis peptide bond; other site 1427342009531 insertion regions; other site 1427342009532 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342009533 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342009534 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342009535 N-terminal plug; other site 1427342009536 ligand-binding site [chemical binding]; other site 1427342009537 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 1427342009538 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342009539 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 1427342009540 inter-subunit interface; other site 1427342009541 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 1427342009542 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 1427342009543 active site 1427342009544 dimer interface [polypeptide binding]; other site 1427342009545 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 1427342009546 Ligand Binding Site [chemical binding]; other site 1427342009547 Molecular Tunnel; other site 1427342009548 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 1427342009549 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 1427342009550 [2Fe-2S] cluster binding site [ion binding]; other site 1427342009551 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 1427342009552 putative alpha subunit interface [polypeptide binding]; other site 1427342009553 putative active site [active] 1427342009554 putative substrate binding site [chemical binding]; other site 1427342009555 Fe binding site [ion binding]; other site 1427342009556 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342009557 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342009558 putative DNA binding site [nucleotide binding]; other site 1427342009559 putative Zn2+ binding site [ion binding]; other site 1427342009560 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342009561 arylformamidase; Region: trp_arylform; TIGR03035 1427342009562 Kynureninase [Amino acid transport and metabolism]; Region: COG3844 1427342009563 kynureninase; Region: kynureninase; TIGR01814 1427342009564 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342009565 catalytic residue [active] 1427342009566 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 1427342009567 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342009568 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009569 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009570 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342009571 dimerization interface [polypeptide binding]; other site 1427342009572 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1427342009573 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_2; cd07580 1427342009574 putative active site [active] 1427342009575 catalytic triad [active] 1427342009576 putative dimer interface [polypeptide binding]; other site 1427342009577 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 1427342009578 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342009579 Na binding site [ion binding]; other site 1427342009580 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3322 1427342009581 PAS domain S-box; Region: sensory_box; TIGR00229 1427342009582 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342009583 putative active site [active] 1427342009584 heme pocket [chemical binding]; other site 1427342009585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342009586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342009587 metal binding site [ion binding]; metal-binding site 1427342009588 active site 1427342009589 I-site; other site 1427342009590 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342009591 elongation factor G; Reviewed; Region: PRK00007 1427342009592 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1427342009593 G1 box; other site 1427342009594 putative GEF interaction site [polypeptide binding]; other site 1427342009595 GTP/Mg2+ binding site [chemical binding]; other site 1427342009596 Switch I region; other site 1427342009597 G2 box; other site 1427342009598 G3 box; other site 1427342009599 Switch II region; other site 1427342009600 G4 box; other site 1427342009601 G5 box; other site 1427342009602 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 1427342009603 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 1427342009604 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 1427342009605 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342009606 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342009607 N-terminal plug; other site 1427342009608 ligand-binding site [chemical binding]; other site 1427342009609 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 1427342009610 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1427342009611 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 1427342009612 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 1427342009613 MFS_1 like family; Region: MFS_1_like; pfam12832 1427342009614 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 1427342009615 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342009616 motif II; other site 1427342009617 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1427342009618 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 1427342009619 putative active site [active] 1427342009620 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 1427342009621 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 1427342009622 Multicopper oxidase; Region: Cu-oxidase; pfam00394 1427342009623 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 1427342009624 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 1427342009625 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: PcoB; COG3667 1427342009626 Uncharacterized conserved protein [Function unknown]; Region: COG3673 1427342009627 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342009628 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1427342009629 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342009630 catalytic residue [active] 1427342009631 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 1427342009632 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342009633 Walker A/P-loop; other site 1427342009634 ATP binding site [chemical binding]; other site 1427342009635 Q-loop/lid; other site 1427342009636 ABC transporter signature motif; other site 1427342009637 Walker B; other site 1427342009638 D-loop; other site 1427342009639 H-loop/switch region; other site 1427342009640 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342009641 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342009642 Walker A/P-loop; other site 1427342009643 ATP binding site [chemical binding]; other site 1427342009644 Q-loop/lid; other site 1427342009645 ABC transporter signature motif; other site 1427342009646 Walker B; other site 1427342009647 D-loop; other site 1427342009648 H-loop/switch region; other site 1427342009649 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342009650 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 1427342009651 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342009652 dimer interface [polypeptide binding]; other site 1427342009653 conserved gate region; other site 1427342009654 ABC-ATPase subunit interface; other site 1427342009655 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 1427342009656 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342009657 dimer interface [polypeptide binding]; other site 1427342009658 conserved gate region; other site 1427342009659 ABC-ATPase subunit interface; other site 1427342009660 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 1427342009661 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 1427342009662 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342009663 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342009664 N-terminal plug; other site 1427342009665 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342009666 ligand-binding site [chemical binding]; other site 1427342009667 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009668 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009669 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342009670 putative effector binding pocket; other site 1427342009671 dimerization interface [polypeptide binding]; other site 1427342009672 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342009673 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009674 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 1427342009675 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009676 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; Region: PBP2_CynR; cd08425 1427342009677 dimerization interface [polypeptide binding]; other site 1427342009678 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 1427342009679 active site clefts [active] 1427342009680 zinc binding site [ion binding]; other site 1427342009681 dimer interface [polypeptide binding]; other site 1427342009682 cyanate hydratase; Validated; Region: PRK02866 1427342009683 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 1427342009684 oligomer interface [polypeptide binding]; other site 1427342009685 active site 1427342009686 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342009687 FecR protein; Region: FecR; pfam04773 1427342009688 RNA polymerase sigma factor; Provisional; Region: PRK12525 1427342009689 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342009690 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342009691 DNA binding residues [nucleotide binding] 1427342009692 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1427342009693 metal binding site [ion binding]; metal-binding site 1427342009694 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 1427342009695 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 1427342009696 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342009697 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 1427342009698 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342009699 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342009700 Haemolytic domain; Region: Haemolytic; pfam01809 1427342009701 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 1427342009702 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1427342009703 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 1427342009704 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1427342009705 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 1427342009706 probable active site [active] 1427342009707 serine/threonine transporter SstT; Provisional; Region: PRK13628 1427342009708 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1427342009709 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342009710 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342009711 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 1427342009712 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342009713 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 1427342009714 Predicted membrane protein [Function unknown]; Region: COG4392 1427342009715 thiamine pyrophosphate protein; Validated; Region: PRK08199 1427342009716 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342009717 PYR/PP interface [polypeptide binding]; other site 1427342009718 dimer interface [polypeptide binding]; other site 1427342009719 TPP binding site [chemical binding]; other site 1427342009720 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342009721 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 1427342009722 TPP-binding site [chemical binding]; other site 1427342009723 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 1427342009724 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 1427342009725 FAD binding pocket [chemical binding]; other site 1427342009726 FAD binding motif [chemical binding]; other site 1427342009727 phosphate binding motif [ion binding]; other site 1427342009728 NAD binding pocket [chemical binding]; other site 1427342009729 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342009730 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342009731 DNA-binding site [nucleotide binding]; DNA binding site 1427342009732 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342009733 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342009734 homodimer interface [polypeptide binding]; other site 1427342009735 catalytic residue [active] 1427342009736 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 1427342009737 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342009738 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342009739 putative DNA binding site [nucleotide binding]; other site 1427342009740 putative Zn2+ binding site [ion binding]; other site 1427342009741 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342009742 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 1427342009743 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 1427342009744 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342009745 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 1427342009746 active site 1427342009747 metal binding site [ion binding]; metal-binding site 1427342009748 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 1427342009749 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 1427342009750 active site 1427342009751 tetramer interface; other site 1427342009752 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1427342009753 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1427342009754 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1427342009755 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 1427342009756 Protein of unknown function (DUF3203); Region: DUF3203; pfam11462 1427342009757 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342009758 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342009759 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 1427342009760 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 1427342009761 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342009762 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342009763 multidrug efflux protein; Reviewed; Region: PRK09577 1427342009764 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342009765 SdiA-regulated; Region: SdiA-regulated; pfam06977 1427342009766 SdiA-regulated; Region: SdiA-regulated; cd09971 1427342009767 putative active site [active] 1427342009768 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 1427342009769 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1427342009770 DNA binding residues [nucleotide binding] 1427342009771 putative dimer interface [polypeptide binding]; other site 1427342009772 isovaleryl-CoA dehydrogenase; Region: PLN02519 1427342009773 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 1427342009774 substrate binding site [chemical binding]; other site 1427342009775 FAD binding site [chemical binding]; other site 1427342009776 catalytic base [active] 1427342009777 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 1427342009778 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1427342009779 gamma-carboxygeranoyl-CoA hydratase; Validated; Region: PRK05674 1427342009780 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342009781 substrate binding site [chemical binding]; other site 1427342009782 oxyanion hole (OAH) forming residues; other site 1427342009783 trimer interface [polypeptide binding]; other site 1427342009784 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1427342009785 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342009786 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342009787 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 1427342009788 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342009789 carboxyltransferase (CT) interaction site; other site 1427342009790 biotinylation site [posttranslational modification]; other site 1427342009791 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 1427342009792 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 1427342009793 active site 1427342009794 catalytic residues [active] 1427342009795 metal binding site [ion binding]; metal-binding site 1427342009796 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 1427342009797 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342009798 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342009799 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 1427342009800 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 1427342009801 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 1427342009802 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1427342009803 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 1427342009804 C-terminal domain interface [polypeptide binding]; other site 1427342009805 GSH binding site (G-site) [chemical binding]; other site 1427342009806 maleylacetoacetate isomerase; Region: maiA; TIGR01262 1427342009807 putative dimer interface [polypeptide binding]; other site 1427342009808 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 1427342009809 dimer interface [polypeptide binding]; other site 1427342009810 N-terminal domain interface [polypeptide binding]; other site 1427342009811 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 1427342009812 benzoate transport; Region: 2A0115; TIGR00895 1427342009813 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009814 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009815 PAS domain; Region: PAS; smart00091 1427342009816 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 1427342009817 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342009818 Walker B motif; other site 1427342009819 arginine finger; other site 1427342009820 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342009821 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 1427342009822 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 1427342009823 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 1427342009824 NAD binding site [chemical binding]; other site 1427342009825 homotetramer interface [polypeptide binding]; other site 1427342009826 homodimer interface [polypeptide binding]; other site 1427342009827 substrate binding site [chemical binding]; other site 1427342009828 active site 1427342009829 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 1427342009830 acetyl-CoA acetyltransferase; Provisional; Region: PRK05656 1427342009831 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342009832 dimer interface [polypeptide binding]; other site 1427342009833 active site 1427342009834 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1427342009835 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1427342009836 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342009837 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009838 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 1427342009839 putative dimerization interface [polypeptide binding]; other site 1427342009840 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 1427342009841 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 1427342009842 acyl-activating enzyme (AAE) consensus motif; other site 1427342009843 putative AMP binding site [chemical binding]; other site 1427342009844 putative active site [active] 1427342009845 putative CoA binding site [chemical binding]; other site 1427342009846 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 1427342009847 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 1427342009848 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3554 1427342009849 major facilitator superfamily transporter; Provisional; Region: PRK05122 1427342009850 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342009851 putative substrate translocation pore; other site 1427342009852 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 1427342009853 PAS domain S-box; Region: sensory_box; TIGR00229 1427342009854 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 1427342009855 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342009856 dimer interface [polypeptide binding]; other site 1427342009857 phosphorylation site [posttranslational modification] 1427342009858 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342009859 ATP binding site [chemical binding]; other site 1427342009860 G-X-G motif; other site 1427342009861 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342009862 active site 1427342009863 phosphorylation site [posttranslational modification] 1427342009864 intermolecular recognition site; other site 1427342009865 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH4; cd08188 1427342009866 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1427342009867 putative active site [active] 1427342009868 metal binding site [ion binding]; metal-binding site 1427342009869 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1427342009870 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342009871 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 1427342009872 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342009873 FeS/SAM binding site; other site 1427342009874 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 1427342009875 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional; Region: PRK02079 1427342009876 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 1427342009877 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 1427342009878 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 1427342009879 coenzyme PQQ synthesis protein PqqA; Provisional; Region: pqqA; PRK00284 1427342009880 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1427342009881 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342009882 NAD(P) binding site [chemical binding]; other site 1427342009883 catalytic residues [active] 1427342009884 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342009885 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342009886 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 1427342009887 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 1427342009888 dimer interface [polypeptide binding]; other site 1427342009889 Trp docking motif [polypeptide binding]; other site 1427342009890 active site 1427342009891 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1427342009892 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1427342009893 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1427342009894 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1427342009895 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1427342009896 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1427342009897 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342009898 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342009899 active site 1427342009900 phosphorylation site [posttranslational modification] 1427342009901 intermolecular recognition site; other site 1427342009902 dimerization interface [polypeptide binding]; other site 1427342009903 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342009904 DNA binding residues [nucleotide binding] 1427342009905 dimerization interface [polypeptide binding]; other site 1427342009906 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 1427342009907 Histidine kinase; Region: HisKA_3; pfam07730 1427342009908 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342009909 ATP binding site [chemical binding]; other site 1427342009910 Mg2+ binding site [ion binding]; other site 1427342009911 G-X-G motif; other site 1427342009912 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342009913 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342009914 active site 1427342009915 phosphorylation site [posttranslational modification] 1427342009916 intermolecular recognition site; other site 1427342009917 dimerization interface [polypeptide binding]; other site 1427342009918 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342009919 DNA binding residues [nucleotide binding] 1427342009920 dimerization interface [polypeptide binding]; other site 1427342009921 PAS fold; Region: PAS_7; pfam12860 1427342009922 PAS fold; Region: PAS_7; pfam12860 1427342009923 PAS fold; Region: PAS_4; pfam08448 1427342009924 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342009925 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342009926 dimer interface [polypeptide binding]; other site 1427342009927 phosphorylation site [posttranslational modification] 1427342009928 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342009929 ATP binding site [chemical binding]; other site 1427342009930 Mg2+ binding site [ion binding]; other site 1427342009931 G-X-G motif; other site 1427342009932 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342009933 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342009934 active site 1427342009935 phosphorylation site [posttranslational modification] 1427342009936 intermolecular recognition site; other site 1427342009937 dimerization interface [polypeptide binding]; other site 1427342009938 Uncharacterized conserved protein [Function unknown]; Region: COG3287 1427342009939 FIST N domain; Region: FIST; pfam08495 1427342009940 FIST C domain; Region: FIST_C; pfam10442 1427342009941 Gram-negative porin; Region: Porin_4; pfam13609 1427342009942 coenzyme PQQ biosynthesis probable peptidase PqqF; Region: PQQ_syn_pqqF; TIGR02110 1427342009943 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1427342009944 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1427342009945 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1427342009946 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1427342009947 Sulfatase; Region: Sulfatase; pfam00884 1427342009948 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 1427342009949 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 1427342009950 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 1427342009951 putative substrate binding pocket [chemical binding]; other site 1427342009952 trimer interface [polypeptide binding]; other site 1427342009953 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 1427342009954 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342009955 Walker A/P-loop; other site 1427342009956 ATP binding site [chemical binding]; other site 1427342009957 Q-loop/lid; other site 1427342009958 ABC transporter signature motif; other site 1427342009959 Walker B; other site 1427342009960 D-loop; other site 1427342009961 H-loop/switch region; other site 1427342009962 ABC transporter; Region: ABC_tran_2; pfam12848 1427342009963 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342009964 azoreductase; Reviewed; Region: PRK00170 1427342009965 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342009966 LysR family transcriptional regulator; Provisional; Region: PRK14997 1427342009967 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342009968 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342009969 dimerization interface [polypeptide binding]; other site 1427342009970 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342009971 DNA-binding site [nucleotide binding]; DNA binding site 1427342009972 RNA-binding motif; other site 1427342009973 Predicted membrane protein [Function unknown]; Region: COG3326 1427342009974 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 1427342009975 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 1427342009976 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; COG3172 1427342009977 AAA domain; Region: AAA_28; pfam13521 1427342009978 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 1427342009979 putative active site [active] 1427342009980 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 1427342009981 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1427342009982 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 1427342009983 substrate binding site [chemical binding]; other site 1427342009984 dimer interface [polypeptide binding]; other site 1427342009985 ATP binding site [chemical binding]; other site 1427342009986 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1427342009987 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1427342009988 DNA binding site [nucleotide binding] 1427342009989 domain linker motif; other site 1427342009990 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 1427342009991 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342009992 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 1427342009993 TM-ABC transporter signature motif; other site 1427342009994 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 1427342009995 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 1427342009996 Walker A/P-loop; other site 1427342009997 ATP binding site [chemical binding]; other site 1427342009998 Q-loop/lid; other site 1427342009999 ABC transporter signature motif; other site 1427342010000 Walker B; other site 1427342010001 D-loop; other site 1427342010002 H-loop/switch region; other site 1427342010003 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1427342010004 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 1427342010005 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 1427342010006 ligand binding site [chemical binding]; other site 1427342010007 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342010008 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010009 Walker A motif; other site 1427342010010 ATP binding site [chemical binding]; other site 1427342010011 Walker B motif; other site 1427342010012 arginine finger; other site 1427342010013 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342010014 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 1427342010015 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 1427342010016 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342010017 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342010018 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342010019 Coenzyme A binding pocket [chemical binding]; other site 1427342010020 Peptidase_C39 like family; Region: DUF3335; pfam11814 1427342010021 Catalase-like heme-binding proteins similar to the uncharacterized y4iL; Region: y4iL_like; cd08152 1427342010022 putative heme binding pocket [chemical binding]; other site 1427342010023 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342010024 AAA domain; Region: AAA_21; pfam13304 1427342010025 Walker A/P-loop; other site 1427342010026 ATP binding site [chemical binding]; other site 1427342010027 AAA domain; Region: AAA_21; pfam13304 1427342010028 Domain of unknown function (DUF4354); Region: DUF4354; pfam14263 1427342010029 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342010030 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1427342010031 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342010032 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 1427342010033 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 1427342010034 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1427342010035 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342010036 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342010037 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1427342010038 putative active site [active] 1427342010039 heme pocket [chemical binding]; other site 1427342010040 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342010041 putative active site [active] 1427342010042 heme pocket [chemical binding]; other site 1427342010043 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342010044 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342010045 dimer interface [polypeptide binding]; other site 1427342010046 putative CheW interface [polypeptide binding]; other site 1427342010047 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1427342010048 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1427342010049 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 1427342010050 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 1427342010051 THF binding site; other site 1427342010052 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 1427342010053 substrate binding site [chemical binding]; other site 1427342010054 THF binding site; other site 1427342010055 zinc-binding site [ion binding]; other site 1427342010056 YcaO domain protein; Region: TIGR03549 1427342010057 OsmC-like protein; Region: OsmC; pfam02566 1427342010058 YcaO-like family; Region: YcaO; pfam02624 1427342010059 Uncharacterized conserved protein [Function unknown]; Region: COG4744 1427342010060 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1427342010061 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 1427342010062 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 1427342010063 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 1427342010064 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 1427342010065 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342010066 N-terminal plug; other site 1427342010067 ligand-binding site [chemical binding]; other site 1427342010068 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342010069 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342010070 S-adenosylmethionine binding site [chemical binding]; other site 1427342010071 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 1427342010072 ATP cone domain; Region: ATP-cone; pfam03477 1427342010073 Class III ribonucleotide reductase; Region: RNR_III; cd01675 1427342010074 effector binding site; other site 1427342010075 active site 1427342010076 Zn binding site [ion binding]; other site 1427342010077 glycine loop; other site 1427342010078 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 1427342010079 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 1427342010080 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342010081 FeS/SAM binding site; other site 1427342010082 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342010083 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342010084 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 1427342010085 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 1427342010086 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1427342010087 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2508 1427342010088 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1427342010089 Protein of unknown function (DUF2599); Region: DUF2599; pfam10783 1427342010090 RNA polymerase sigma factor; Provisional; Region: PRK12528 1427342010091 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342010092 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342010093 DNA binding residues [nucleotide binding] 1427342010094 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342010095 FecR protein; Region: FecR; pfam04773 1427342010096 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342010097 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342010098 N-terminal plug; other site 1427342010099 ligand-binding site [chemical binding]; other site 1427342010100 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342010101 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 1427342010102 RNA polymerase Rpb5, C-terminal domain; Region: RNA_pol_Rpb5_C; cl00883 1427342010103 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342010104 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342010105 putative substrate translocation pore; other site 1427342010106 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342010107 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 1427342010108 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 1427342010109 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 1427342010110 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 1427342010111 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 1427342010112 Phenazine biosynthesis-like protein; Region: PhzC-PhzF; pfam02567 1427342010113 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 1427342010114 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1427342010115 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1427342010116 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1427342010117 glutamine binding [chemical binding]; other site 1427342010118 catalytic triad [active] 1427342010119 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 1427342010120 hydrophobic substrate binding pocket; other site 1427342010121 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342010122 active site 1427342010123 conserved cis-peptide bond; other site 1427342010124 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 1427342010125 Phenazine biosynthesis protein A/B; Region: PHZA_PHZB; pfam03284 1427342010126 Phenazine biosynthesis protein A/B; Region: PHZA_PHZB; pfam03284 1427342010127 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 1427342010128 Autoinducer binding domain; Region: Autoind_bind; pfam03472 1427342010129 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342010130 DNA binding residues [nucleotide binding] 1427342010131 dimerization interface [polypeptide binding]; other site 1427342010132 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 1427342010133 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 1427342010134 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 1427342010135 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 1427342010136 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 1427342010137 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 1427342010138 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 1427342010139 active site 1427342010140 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342010141 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 1427342010142 putative C-terminal domain interface [polypeptide binding]; other site 1427342010143 putative GSH binding site (G-site) [chemical binding]; other site 1427342010144 putative dimer interface [polypeptide binding]; other site 1427342010145 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 1427342010146 putative N-terminal domain interface [polypeptide binding]; other site 1427342010147 putative dimer interface [polypeptide binding]; other site 1427342010148 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342010149 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342010150 DNA polymerase II; Reviewed; Region: PRK05762 1427342010151 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 1427342010152 active site 1427342010153 catalytic site [active] 1427342010154 substrate binding site [chemical binding]; other site 1427342010155 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 1427342010156 active site 1427342010157 metal-binding site 1427342010158 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342010159 Coenzyme A binding pocket [chemical binding]; other site 1427342010160 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1427342010161 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1427342010162 sequence-specific DNA binding site [nucleotide binding]; other site 1427342010163 salt bridge; other site 1427342010164 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1427342010165 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 1427342010166 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1427342010167 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342010168 catalytic loop [active] 1427342010169 iron binding site [ion binding]; other site 1427342010170 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342010171 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342010172 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342010173 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1427342010174 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342010175 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342010176 non-specific DNA binding site [nucleotide binding]; other site 1427342010177 salt bridge; other site 1427342010178 sequence-specific DNA binding site [nucleotide binding]; other site 1427342010179 HD domain; Region: HD_3; pfam13023 1427342010180 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1427342010181 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342010182 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342010183 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 1427342010184 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 1427342010185 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342010186 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342010187 Walker A/P-loop; other site 1427342010188 ATP binding site [chemical binding]; other site 1427342010189 Q-loop/lid; other site 1427342010190 ABC transporter signature motif; other site 1427342010191 Walker B; other site 1427342010192 D-loop; other site 1427342010193 H-loop/switch region; other site 1427342010194 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342010195 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 1427342010196 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 1427342010197 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1427342010198 Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily; Region: ZntB_u1; cd12834 1427342010199 Cl binding site [ion binding]; other site 1427342010200 oligomer interface [polypeptide binding]; other site 1427342010201 EcsC protein family; Region: EcsC; pfam12787 1427342010202 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1427342010203 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342010204 acyl carrier protein; Provisional; Region: acpP; PRK00982 1427342010205 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 1427342010206 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342010207 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342010208 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342010209 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342010210 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 1427342010211 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 1427342010212 DEAD_2; Region: DEAD_2; pfam06733 1427342010213 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 1427342010214 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 1427342010215 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 1427342010216 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342010217 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 1427342010218 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 1427342010219 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342010220 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 1427342010221 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342010222 dimer interface [polypeptide binding]; other site 1427342010223 conserved gate region; other site 1427342010224 putative PBP binding loops; other site 1427342010225 ABC-ATPase subunit interface; other site 1427342010226 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 1427342010227 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342010228 Walker A/P-loop; other site 1427342010229 ATP binding site [chemical binding]; other site 1427342010230 Q-loop/lid; other site 1427342010231 ABC transporter signature motif; other site 1427342010232 Walker B; other site 1427342010233 D-loop; other site 1427342010234 H-loop/switch region; other site 1427342010235 TOBE domain; Region: TOBE; cl01440 1427342010236 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 1427342010237 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 1427342010238 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342010239 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342010240 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 1427342010241 putative effector binding pocket; other site 1427342010242 dimerization interface [polypeptide binding]; other site 1427342010243 Streptomycin 6-kinase [Defense mechanisms]; Region: StrB; COG3570 1427342010244 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342010245 Protein of unknown function (DUF808); Region: DUF808; pfam05661 1427342010246 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 1427342010247 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1427342010248 Low-spin heme binding site [chemical binding]; other site 1427342010249 Putative water exit pathway; other site 1427342010250 Binuclear center (active site) [active] 1427342010251 Putative proton exit pathway; other site 1427342010252 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 1427342010253 HPP family; Region: HPP; pfam04982 1427342010254 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 1427342010255 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342010256 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342010257 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342010258 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342010259 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342010260 metal binding site [ion binding]; metal-binding site 1427342010261 active site 1427342010262 I-site; other site 1427342010263 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 1427342010264 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 1427342010265 conserved cys residue [active] 1427342010266 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342010267 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342010268 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 1427342010269 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 1427342010270 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342010271 putative substrate translocation pore; other site 1427342010272 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1427342010273 IscR-regulated protein YhgI; Region: YhgI_GntY; TIGR03341 1427342010274 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1427342010275 Cytochrome c; Region: Cytochrom_C; cl11414 1427342010276 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 1427342010277 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 1427342010278 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 1427342010279 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1427342010280 substrate binding pocket [chemical binding]; other site 1427342010281 dimer interface [polypeptide binding]; other site 1427342010282 inhibitor binding site; inhibition site 1427342010283 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 1427342010284 B12 binding site [chemical binding]; other site 1427342010285 cobalt ligand [ion binding]; other site 1427342010286 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 1427342010287 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3171 1427342010288 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 1427342010289 putative deacylase active site [active] 1427342010290 Domain of unknown function (DUF1883); Region: DUF1883; pfam08980 1427342010291 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 1427342010292 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 1427342010293 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 1427342010294 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342010295 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342010296 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3749 1427342010297 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342010298 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342010299 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342010300 CoenzymeA binding site [chemical binding]; other site 1427342010301 subunit interaction site [polypeptide binding]; other site 1427342010302 PHB binding site; other site 1427342010303 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 1427342010304 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342010305 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 1427342010306 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 1427342010307 NADP binding site [chemical binding]; other site 1427342010308 dimer interface [polypeptide binding]; other site 1427342010309 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 1427342010310 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1427342010311 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1427342010312 tandem repeat interface [polypeptide binding]; other site 1427342010313 oligomer interface [polypeptide binding]; other site 1427342010314 active site residues [active] 1427342010315 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 1427342010316 catalytic core [active] 1427342010317 Putative sterol carrier protein [Lipid metabolism]; Region: COG3255 1427342010318 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342010319 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 1427342010320 putative active site [active] 1427342010321 putative substrate binding site [chemical binding]; other site 1427342010322 ATP binding site [chemical binding]; other site 1427342010323 short chain dehydrogenase; Provisional; Region: PRK07035 1427342010324 classical (c) SDRs; Region: SDR_c; cd05233 1427342010325 NAD(P) binding site [chemical binding]; other site 1427342010326 active site 1427342010327 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 1427342010328 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342010329 NAD(P) binding site [chemical binding]; other site 1427342010330 active site 1427342010331 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 1427342010332 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342010333 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342010334 dimerization interface [polypeptide binding]; other site 1427342010335 substrate binding pocket [chemical binding]; other site 1427342010336 hypothetical protein; Provisional; Region: PRK10621 1427342010337 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1427342010338 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 1427342010339 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 1427342010340 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 1427342010341 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 1427342010342 putative NADH binding site [chemical binding]; other site 1427342010343 putative active site [active] 1427342010344 nudix motif; other site 1427342010345 putative metal binding site [ion binding]; other site 1427342010346 enoyl-CoA hydratase; Provisional; Region: PRK06142 1427342010347 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342010348 substrate binding site [chemical binding]; other site 1427342010349 oxyanion hole (OAH) forming residues; other site 1427342010350 trimer interface [polypeptide binding]; other site 1427342010351 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 1427342010352 arginine:agmatin antiporter; Provisional; Region: PRK10644 1427342010353 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 1427342010354 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 1427342010355 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 1427342010356 homodimer interface [polypeptide binding]; other site 1427342010357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342010358 catalytic residue [active] 1427342010359 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 1427342010360 Ketosteroid isomerase-related protein [General function prediction only]; Region: COG3631 1427342010361 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 1427342010362 active site 1427342010363 catalytic site [active] 1427342010364 substrate binding site [chemical binding]; other site 1427342010365 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1427342010366 RNA/DNA hybrid binding site [nucleotide binding]; other site 1427342010367 active site 1427342010368 Methyltransferase domain; Region: Methyltransf_11; pfam08241 1427342010369 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 1427342010370 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 1427342010371 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342010372 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342010373 catalytic residue [active] 1427342010374 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342010375 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342010376 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342010377 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 1427342010378 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 1427342010379 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 1427342010380 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 1427342010381 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 1427342010382 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342010383 dimer interface [polypeptide binding]; other site 1427342010384 conserved gate region; other site 1427342010385 putative PBP binding loops; other site 1427342010386 ABC-ATPase subunit interface; other site 1427342010387 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 1427342010388 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 1427342010389 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342010390 dimer interface [polypeptide binding]; other site 1427342010391 conserved gate region; other site 1427342010392 putative PBP binding loops; other site 1427342010393 ABC-ATPase subunit interface; other site 1427342010394 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 1427342010395 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342010396 Walker A/P-loop; other site 1427342010397 ATP binding site [chemical binding]; other site 1427342010398 Q-loop/lid; other site 1427342010399 ABC transporter signature motif; other site 1427342010400 Walker B; other site 1427342010401 D-loop; other site 1427342010402 H-loop/switch region; other site 1427342010403 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342010404 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342010405 Walker A/P-loop; other site 1427342010406 ATP binding site [chemical binding]; other site 1427342010407 Q-loop/lid; other site 1427342010408 ABC transporter signature motif; other site 1427342010409 Walker B; other site 1427342010410 D-loop; other site 1427342010411 H-loop/switch region; other site 1427342010412 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342010413 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 1427342010414 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1427342010415 NAD binding site [chemical binding]; other site 1427342010416 homotetramer interface [polypeptide binding]; other site 1427342010417 homodimer interface [polypeptide binding]; other site 1427342010418 substrate binding site [chemical binding]; other site 1427342010419 active site 1427342010420 periplasmic folding chaperone; Provisional; Region: PRK10788 1427342010421 SurA N-terminal domain; Region: SurA_N_3; pfam13624 1427342010422 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1427342010423 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 1427342010424 IHF dimer interface [polypeptide binding]; other site 1427342010425 IHF - DNA interface [nucleotide binding]; other site 1427342010426 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1427342010427 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1427342010428 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010429 Walker A motif; other site 1427342010430 ATP binding site [chemical binding]; other site 1427342010431 Walker B motif; other site 1427342010432 arginine finger; other site 1427342010433 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1427342010434 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1427342010435 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1427342010436 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010437 Walker A motif; other site 1427342010438 ATP binding site [chemical binding]; other site 1427342010439 Walker B motif; other site 1427342010440 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1427342010441 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1427342010442 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1427342010443 oligomer interface [polypeptide binding]; other site 1427342010444 active site residues [active] 1427342010445 trigger factor; Provisional; Region: tig; PRK01490 1427342010446 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342010447 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1427342010448 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 1427342010449 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342010450 active site 1427342010451 phosphorylation site [posttranslational modification] 1427342010452 intermolecular recognition site; other site 1427342010453 dimerization interface [polypeptide binding]; other site 1427342010454 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342010455 DNA binding site [nucleotide binding] 1427342010456 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342010457 dimerization interface [polypeptide binding]; other site 1427342010458 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342010459 dimer interface [polypeptide binding]; other site 1427342010460 phosphorylation site [posttranslational modification] 1427342010461 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342010462 ATP binding site [chemical binding]; other site 1427342010463 Mg2+ binding site [ion binding]; other site 1427342010464 G-X-G motif; other site 1427342010465 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342010466 Beta-lactamase; Region: Beta-lactamase; pfam00144 1427342010467 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 1427342010468 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1427342010469 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1427342010470 homodimer interface [polypeptide binding]; other site 1427342010471 NADP binding site [chemical binding]; other site 1427342010472 substrate binding site [chemical binding]; other site 1427342010473 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1427342010474 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1427342010475 active site 1427342010476 HIGH motif; other site 1427342010477 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1427342010478 KMSKS motif; other site 1427342010479 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 1427342010480 tRNA binding surface [nucleotide binding]; other site 1427342010481 anticodon binding site; other site 1427342010482 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 1427342010483 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1427342010484 active site 1427342010485 HIGH motif; other site 1427342010486 nucleotide binding site [chemical binding]; other site 1427342010487 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 1427342010488 KMSKS motif; other site 1427342010489 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 1427342010490 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 1427342010491 substrate binding site [chemical binding]; other site 1427342010492 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1427342010493 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1427342010494 putative active site [active] 1427342010495 putative metal binding site [ion binding]; other site 1427342010496 SPFH domain / Band 7 family; Region: Band_7; pfam01145 1427342010497 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 1427342010498 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 1427342010499 active site 1427342010500 dinuclear metal binding site [ion binding]; other site 1427342010501 dimerization interface [polypeptide binding]; other site 1427342010502 universal stress protein UspE; Provisional; Region: PRK11175 1427342010503 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342010504 Ligand Binding Site [chemical binding]; other site 1427342010505 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342010506 Ligand Binding Site [chemical binding]; other site 1427342010507 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 1427342010508 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 1427342010509 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 1427342010510 substrate binding site [chemical binding]; other site 1427342010511 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 1427342010512 substrate binding site [chemical binding]; other site 1427342010513 ligand binding site [chemical binding]; other site 1427342010514 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 1427342010515 NMT1-like family; Region: NMT1_2; pfam13379 1427342010516 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 1427342010517 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342010518 active site 1427342010519 phosphorylation site [posttranslational modification] 1427342010520 intermolecular recognition site; other site 1427342010521 dimerization interface [polypeptide binding]; other site 1427342010522 ANTAR domain; Region: ANTAR; pfam03861 1427342010523 Alginate lyase; Region: Alginate_lyase2; pfam08787 1427342010524 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 1427342010525 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342010526 putative substrate translocation pore; other site 1427342010527 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 1427342010528 Protein kinase domain; Region: Pkinase; pfam00069 1427342010529 Catalytic domain of Protein Kinases; Region: PKc; cd00180 1427342010530 active site 1427342010531 ATP binding site [chemical binding]; other site 1427342010532 substrate binding site [chemical binding]; other site 1427342010533 activation loop (A-loop); other site 1427342010534 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 1427342010535 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342010536 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1427342010537 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1427342010538 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1427342010539 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 1427342010540 [2Fe-2S] cluster binding site [ion binding]; other site 1427342010541 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 1427342010542 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 1427342010543 [4Fe-4S] binding site [ion binding]; other site 1427342010544 molybdopterin cofactor binding site; other site 1427342010545 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 1427342010546 molybdopterin cofactor binding site; other site 1427342010547 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 1427342010548 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1427342010549 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 1427342010550 active site 1427342010551 SAM binding site [chemical binding]; other site 1427342010552 homodimer interface [polypeptide binding]; other site 1427342010553 OprF membrane domain; Region: OprF; pfam05736 1427342010554 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342010555 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342010556 ligand binding site [chemical binding]; other site 1427342010557 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1427342010558 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342010559 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342010560 DNA binding residues [nucleotide binding] 1427342010561 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342010562 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1427342010563 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 1427342010564 Cl binding site [ion binding]; other site 1427342010565 oligomer interface [polypeptide binding]; other site 1427342010566 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 1427342010567 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342010568 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1427342010569 phosphoenolpyruvate synthase; Validated; Region: PRK06464 1427342010570 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1427342010571 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1427342010572 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1427342010573 PEP synthetase regulatory protein; Provisional; Region: PRK05339 1427342010574 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 1427342010575 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 1427342010576 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 1427342010577 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 1427342010578 Maltose operon periplasmic protein precursor (MalM); Region: MalM; pfam07148 1427342010579 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 1427342010580 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 1427342010581 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 1427342010582 putative active site [active] 1427342010583 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 1427342010584 AAA ATPase domain; Region: AAA_16; pfam13191 1427342010585 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342010586 DNA binding residues [nucleotide binding] 1427342010587 dimerization interface [polypeptide binding]; other site 1427342010588 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 1427342010589 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342010590 DNA binding residues [nucleotide binding] 1427342010591 dimerization interface [polypeptide binding]; other site 1427342010592 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 1427342010593 aminodeoxychorismate synthase, component I, clade 2; Region: PabB-clade2; TIGR01824 1427342010594 chorismate binding enzyme; Region: Chorismate_bind; cl10555 1427342010595 phosphoserine phosphatase; Provisional; Region: thrH; PRK13582 1427342010596 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 1427342010597 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 1427342010598 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 1427342010599 Active Sites [active] 1427342010600 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 1427342010601 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342010602 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 1427342010603 substrate binding site [chemical binding]; other site 1427342010604 dimerization interface [polypeptide binding]; other site 1427342010605 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342010606 Ligand Binding Site [chemical binding]; other site 1427342010607 2-dehydropantoate 2-reductase; Provisional; Region: PRK06249 1427342010608 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 1427342010609 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 1427342010610 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 1427342010611 catalytic residues [active] 1427342010612 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 1427342010613 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1427342010614 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342010615 Coenzyme A binding pocket [chemical binding]; other site 1427342010616 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 1427342010617 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342010618 substrate binding site [chemical binding]; other site 1427342010619 oxyanion hole (OAH) forming residues; other site 1427342010620 trimer interface [polypeptide binding]; other site 1427342010621 Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Poa1p_like; cd02901 1427342010622 ADP-ribose binding site [chemical binding]; other site 1427342010623 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 1427342010624 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 1427342010625 catalytic triad [active] 1427342010626 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 1427342010627 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 1427342010628 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342010629 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342010630 active site 1427342010631 catalytic tetrad [active] 1427342010632 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342010633 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342010634 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 1427342010635 putative effector binding pocket; other site 1427342010636 putative dimerization interface [polypeptide binding]; other site 1427342010637 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 1427342010638 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342010639 substrate binding site [chemical binding]; other site 1427342010640 oxyanion hole (OAH) forming residues; other site 1427342010641 trimer interface [polypeptide binding]; other site 1427342010642 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342010643 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342010644 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 1427342010645 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342010646 dimer interface [polypeptide binding]; other site 1427342010647 active site 1427342010648 Predicted permeases [General function prediction only]; Region: COG0679 1427342010649 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342010650 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342010651 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 1427342010652 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 1427342010653 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1427342010654 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 1427342010655 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1427342010656 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 1427342010657 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 1427342010658 Uncharacterized conserved protein [Function unknown]; Region: COG2308 1427342010659 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 1427342010660 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 1427342010661 catalytic triad [active] 1427342010662 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 1427342010663 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 1427342010664 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 1427342010665 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 1427342010666 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342010667 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342010668 metal binding site [ion binding]; metal-binding site 1427342010669 active site 1427342010670 I-site; other site 1427342010671 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342010672 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 1427342010673 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 1427342010674 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1427342010675 Switch II region; other site 1427342010676 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 1427342010677 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 1427342010678 Flagellar assembly protein FliH; Region: FliH; pfam02108 1427342010679 YOP proteins translocation protein K (YscK); Region: YscK; pfam06578 1427342010680 Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]; Region: EscJ; COG4669 1427342010681 type III secretion apparatus protein, YscI/HrpB, C-terminal domain; Region: yscI_hrpB_dom; TIGR02497 1427342010682 YopR Core; Region: YopR_core; cl07585 1427342010683 Bacterial type II secretion system chaperone protein (type_III_yscG); Region: Type_III_YscG; pfam09477 1427342010684 Type III secretion needle MxiH like; Region: MxiH; cl09641 1427342010685 type III secretion apparatus protein, YscD/HrpQ family; Region: type_III_yscD; TIGR02500 1427342010686 type III secretion outer membrane pore, YscC/HrcC family; Region: type_III_yscC; TIGR02516 1427342010687 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342010688 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342010689 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342010690 Tir chaperone protein (CesT) family; Region: CesT; cl08444 1427342010691 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 1427342010692 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342010693 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342010694 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342010695 type III secretion system chaperone YscW; Region: YscW; TIGR02567 1427342010696 Tir chaperone protein (CesT) family; Region: CesT; pfam05932 1427342010697 YopD protein; Region: YopD; pfam05844 1427342010698 Uncharacterized conserved protein [Function unknown]; Region: COG5613 1427342010699 type III secretion low calcium response chaperone LcrH/SycD; Region: LcrH_SycD; TIGR02552 1427342010700 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342010701 binding surface 1427342010702 TPR motif; other site 1427342010703 V antigen (LcrV) protein; Region: LcrV; pfam04792 1427342010704 LcrG protein; Region: LcrG; cl06311 1427342010705 type III secretion system regulator LcrR; Region: LcrR; TIGR02572 1427342010706 Type III secretory pathway, component EscV [Intracellular trafficking and secretion]; Region: EscV; COG4789 1427342010707 FHIPEP family; Region: FHIPEP; pfam00771 1427342010708 Type III secretion system YscX (type_III_YscX); Region: Type_III_YscX; cl09710 1427342010709 type III secretion chaperone SycN; Region: type_III_SycN; TIGR02503 1427342010710 TyeA; Region: TyeA; pfam09059 1427342010711 type III secretion regulator YopN/LcrE/InvE/MxiC; Region: LcrE; TIGR02568 1427342010712 type III secretion system ATPase; Provisional; Region: PRK06936 1427342010713 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1427342010714 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 1427342010715 Walker A motif/ATP binding site; other site 1427342010716 Walker B motif; other site 1427342010717 Type III secretion protein YscO; Region: YscO; pfam07321 1427342010718 type III secretion system needle length determinant; Region: type_III_yscP; TIGR02514 1427342010719 type III secretion system protein; Validated; Region: PRK06933 1427342010720 Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliN; COG1886 1427342010721 Type III secretory pathway, component EscR [Intracellular trafficking and secretion]; Region: EscR; COG4790 1427342010722 Type III secretory pathway, component EscS [Intracellular trafficking and secretion]; Region: EscS; COG4794 1427342010723 Type III secretory pathway, component EscT [Intracellular trafficking and secretion]; Region: EscT; COG4791 1427342010724 Type III secretory pathway, component EscU [Intracellular trafficking and secretion]; Region: EscU; COG4792 1427342010725 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 1427342010726 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 1427342010727 Sulfatase; Region: Sulfatase; pfam00884 1427342010728 Uncharacterized conserved protein [Function unknown]; Region: COG3391 1427342010729 Strictosidine synthase; Region: Str_synth; pfam03088 1427342010730 spermidine synthase; Provisional; Region: PRK00811 1427342010731 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342010732 S-adenosylmethionine binding site [chemical binding]; other site 1427342010733 AlkA N-terminal domain; Region: AlkA_N; pfam06029 1427342010734 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 1427342010735 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1427342010736 minor groove reading motif; other site 1427342010737 helix-hairpin-helix signature motif; other site 1427342010738 substrate binding pocket [chemical binding]; other site 1427342010739 active site 1427342010740 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 1427342010741 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342010742 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 1427342010743 Cupin domain; Region: Cupin_2; cl17218 1427342010744 methylthioribulose-1-phosphate dehydratase; Provisional; Region: PRK09220 1427342010745 intersubunit interface [polypeptide binding]; other site 1427342010746 active site 1427342010747 Zn2+ binding site [ion binding]; other site 1427342010748 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342010749 putative substrate translocation pore; other site 1427342010750 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 1427342010751 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 1427342010752 Tetramer interface [polypeptide binding]; other site 1427342010753 active site 1427342010754 FMN-binding site [chemical binding]; other site 1427342010755 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 1427342010756 HemK family putative methylases; Region: hemK_fam; TIGR00536 1427342010757 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342010758 S-adenosylmethionine binding site [chemical binding]; other site 1427342010759 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 1427342010760 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342010761 catalytic triad [active] 1427342010762 conserved cis-peptide bond; other site 1427342010763 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 1427342010764 Smr domain; Region: Smr; pfam01713 1427342010765 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 1427342010766 homodecamer interface [polypeptide binding]; other site 1427342010767 GTP cyclohydrolase I; Provisional; Region: PLN03044 1427342010768 active site 1427342010769 putative catalytic site residues [active] 1427342010770 zinc binding site [ion binding]; other site 1427342010771 GTP-CH-I/GFRP interaction surface; other site 1427342010772 Hemerythrin; Region: Hemerythrin; cd12107 1427342010773 Fe binding site [ion binding]; other site 1427342010774 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 1427342010775 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 1427342010776 Catalytic domain of Protein Kinases; Region: PKc; cd00180 1427342010777 active site 1427342010778 ATP binding site [chemical binding]; other site 1427342010779 substrate binding site [chemical binding]; other site 1427342010780 activation loop (A-loop); other site 1427342010781 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1427342010782 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 1427342010783 Protein phosphatase 2C; Region: PP2C; pfam00481 1427342010784 active site 1427342010785 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 1427342010786 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 1427342010787 G1 box; other site 1427342010788 GTP/Mg2+ binding site [chemical binding]; other site 1427342010789 G2 box; other site 1427342010790 Switch I region; other site 1427342010791 G3 box; other site 1427342010792 Switch II region; other site 1427342010793 G4 box; other site 1427342010794 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 1427342010795 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 1427342010796 Type VI protein secretion system component VasF [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3455 1427342010797 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522 1427342010798 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 1427342010799 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3521 1427342010800 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 1427342010801 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 1427342010802 phosphopeptide binding site; other site 1427342010803 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 1427342010804 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 1427342010805 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010806 Walker A motif; other site 1427342010807 ATP binding site [chemical binding]; other site 1427342010808 Walker B motif; other site 1427342010809 arginine finger; other site 1427342010810 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342010811 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 1427342010812 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010813 Walker A motif; other site 1427342010814 ATP binding site [chemical binding]; other site 1427342010815 Walker B motif; other site 1427342010816 arginine finger; other site 1427342010817 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342010818 Walker A motif; other site 1427342010819 ATP binding site [chemical binding]; other site 1427342010820 Walker B motif; other site 1427342010821 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1427342010822 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3520 1427342010823 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 1427342010824 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 1427342010825 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 1427342010826 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 1427342010827 Protein of unknown function (DUF877); Region: DUF877; pfam05943 1427342010828 Protein of unknown function (DUF770); Region: DUF770; pfam05591 1427342010829 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3515 1427342010830 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 1427342010831 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 1427342010832 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342010833 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 1427342010834 putative C-terminal domain interface [polypeptide binding]; other site 1427342010835 putative GSH binding site (G-site) [chemical binding]; other site 1427342010836 putative dimer interface [polypeptide binding]; other site 1427342010837 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 1427342010838 N-terminal domain interface [polypeptide binding]; other site 1427342010839 dimer interface [polypeptide binding]; other site 1427342010840 substrate binding pocket (H-site) [chemical binding]; other site 1427342010841 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 1427342010842 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342010843 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342010844 homodimer interface [polypeptide binding]; other site 1427342010845 catalytic residue [active] 1427342010846 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342010847 MarR family; Region: MarR_2; pfam12802 1427342010848 benzoate transporter; Region: benE; TIGR00843 1427342010849 Benzoate membrane transport protein; Region: BenE; pfam03594 1427342010850 bile acid transporter; Region: bass; TIGR00841 1427342010851 Sodium Bile acid symporter family; Region: SBF; cl17470 1427342010852 short chain dehydrogenase; Provisional; Region: PRK06172 1427342010853 classical (c) SDRs; Region: SDR_c; cd05233 1427342010854 NAD(P) binding site [chemical binding]; other site 1427342010855 active site 1427342010856 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 1427342010857 Prostaglandin dehydrogenases; Region: PGDH; cd05288 1427342010858 NAD(P) binding site [chemical binding]; other site 1427342010859 substrate binding site [chemical binding]; other site 1427342010860 dimer interface [polypeptide binding]; other site 1427342010861 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 1427342010862 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1427342010863 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1427342010864 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 1427342010865 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342010866 dimerization interface [polypeptide binding]; other site 1427342010867 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342010868 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342010869 dimer interface [polypeptide binding]; other site 1427342010870 putative CheW interface [polypeptide binding]; other site 1427342010871 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 1427342010872 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1427342010873 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 1427342010874 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 1427342010875 active site residue [active] 1427342010876 selenophosphate synthetase; Provisional; Region: PRK00943 1427342010877 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 1427342010878 dimerization interface [polypeptide binding]; other site 1427342010879 putative ATP binding site [chemical binding]; other site 1427342010880 hypothetical protein; Provisional; Region: PRK10279 1427342010881 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1427342010882 active site 1427342010883 nucleophile elbow; other site 1427342010884 glutaminase; Provisional; Region: PRK00971 1427342010885 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 1427342010886 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 1427342010887 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342010888 active site 1427342010889 phosphorylation site [posttranslational modification] 1427342010890 intermolecular recognition site; other site 1427342010891 dimerization interface [polypeptide binding]; other site 1427342010892 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342010893 DNA binding site [nucleotide binding] 1427342010894 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 1427342010895 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 1427342010896 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 1427342010897 Ligand Binding Site [chemical binding]; other site 1427342010898 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 1427342010899 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342010900 dimer interface [polypeptide binding]; other site 1427342010901 phosphorylation site [posttranslational modification] 1427342010902 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342010903 ATP binding site [chemical binding]; other site 1427342010904 Mg2+ binding site [ion binding]; other site 1427342010905 G-X-G motif; other site 1427342010906 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 1427342010907 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 1427342010908 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342010909 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1427342010910 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 1427342010911 potassium-transporting ATPase subunit F; Provisional; Region: kdbF; PRK14740 1427342010912 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342010913 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342010914 active site 1427342010915 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 1427342010916 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342010917 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342010918 enoyl-CoA hydratase; Provisional; Region: PRK08138 1427342010919 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342010920 substrate binding site [chemical binding]; other site 1427342010921 oxyanion hole (OAH) forming residues; other site 1427342010922 trimer interface [polypeptide binding]; other site 1427342010923 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 1427342010924 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342010925 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342010926 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342010927 Transcriptional regulators [Transcription]; Region: FadR; COG2186 1427342010928 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342010929 DNA-binding site [nucleotide binding]; DNA binding site 1427342010930 FCD domain; Region: FCD; pfam07729 1427342010931 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 1427342010932 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342010933 putative substrate translocation pore; other site 1427342010934 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 1427342010935 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 1427342010936 C-terminal domain interface [polypeptide binding]; other site 1427342010937 GSH binding site (G-site) [chemical binding]; other site 1427342010938 dimer interface [polypeptide binding]; other site 1427342010939 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 1427342010940 N-terminal domain interface [polypeptide binding]; other site 1427342010941 putative dimer interface [polypeptide binding]; other site 1427342010942 active site 1427342010943 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342010944 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342010945 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1427342010946 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342010947 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342010948 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342010949 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342010950 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342010951 CoenzymeA binding site [chemical binding]; other site 1427342010952 subunit interaction site [polypeptide binding]; other site 1427342010953 PHB binding site; other site 1427342010954 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 1427342010955 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 1427342010956 acyl-activating enzyme (AAE) consensus motif; other site 1427342010957 putative AMP binding site [chemical binding]; other site 1427342010958 putative active site [active] 1427342010959 putative CoA binding site [chemical binding]; other site 1427342010960 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 1427342010961 catalytic core [active] 1427342010962 Domain of unknown function (DUF4389); Region: DUF4389; pfam14333 1427342010963 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1427342010964 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1427342010965 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1427342010966 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342010967 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 1427342010968 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1427342010969 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342010970 dimerization interface [polypeptide binding]; other site 1427342010971 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342010972 dimer interface [polypeptide binding]; other site 1427342010973 phosphorylation site [posttranslational modification] 1427342010974 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342010975 ATP binding site [chemical binding]; other site 1427342010976 Mg2+ binding site [ion binding]; other site 1427342010977 G-X-G motif; other site 1427342010978 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342010979 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342010980 active site 1427342010981 phosphorylation site [posttranslational modification] 1427342010982 intermolecular recognition site; other site 1427342010983 dimerization interface [polypeptide binding]; other site 1427342010984 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 1427342010985 active site 1 [active] 1427342010986 dimer interface [polypeptide binding]; other site 1427342010987 active site 2 [active] 1427342010988 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 1427342010989 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 1427342010990 dimer interface [polypeptide binding]; other site 1427342010991 active site 1427342010992 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1427342010993 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342010994 dimerization interface [polypeptide binding]; other site 1427342010995 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342010996 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342010997 dimer interface [polypeptide binding]; other site 1427342010998 putative CheW interface [polypeptide binding]; other site 1427342010999 Predicted transcriptional regulators [Transcription]; Region: COG1733 1427342011000 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 1427342011001 Domain of unknown function (DUF3859); Region: DUF3859; pfam12975 1427342011002 Amidohydrolase; Region: Amidohydro_2; pfam04909 1427342011003 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342011004 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 1427342011005 membrane-bound complex binding site; other site 1427342011006 hinge residues; other site 1427342011007 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342011008 MarR family; Region: MarR; pfam01047 1427342011009 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1427342011010 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342011011 catalytic loop [active] 1427342011012 iron binding site [ion binding]; other site 1427342011013 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342011014 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342011015 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342011016 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1427342011017 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342011018 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342011019 cytochrome c-550; Provisional; Region: psbV; cl17239 1427342011020 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342011021 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342011022 Cupin domain; Region: Cupin_2; cl17218 1427342011023 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342011024 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342011025 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342011026 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 1427342011027 oligomerization interface [polypeptide binding]; other site 1427342011028 active site 1427342011029 metal binding site [ion binding]; metal-binding site 1427342011030 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 1427342011031 heat shock protein 90; Provisional; Region: PRK05218 1427342011032 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342011033 ATP binding site [chemical binding]; other site 1427342011034 Mg2+ binding site [ion binding]; other site 1427342011035 G-X-G motif; other site 1427342011036 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1427342011037 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342011038 CoenzymeA binding site [chemical binding]; other site 1427342011039 subunit interaction site [polypeptide binding]; other site 1427342011040 PHB binding site; other site 1427342011041 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342011042 CoenzymeA binding site [chemical binding]; other site 1427342011043 subunit interaction site [polypeptide binding]; other site 1427342011044 PHB binding site; other site 1427342011045 Predicted membrane protein [Function unknown]; Region: COG3821 1427342011046 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 1427342011047 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1427342011048 CoA binding domain; Region: CoA_binding; pfam02629 1427342011049 CoA-ligase; Region: Ligase_CoA; pfam00549 1427342011050 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1427342011051 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1427342011052 CoA-ligase; Region: Ligase_CoA; pfam00549 1427342011053 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 1427342011054 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1427342011055 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342011056 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1427342011057 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1427342011058 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342011059 E3 interaction surface; other site 1427342011060 lipoyl attachment site [posttranslational modification]; other site 1427342011061 e3 binding domain; Region: E3_binding; pfam02817 1427342011062 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1427342011063 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1427342011064 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 1427342011065 TPP-binding site [chemical binding]; other site 1427342011066 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1427342011067 PYR/PP interface [polypeptide binding]; other site 1427342011068 dimer interface [polypeptide binding]; other site 1427342011069 TPP binding site [chemical binding]; other site 1427342011070 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1427342011071 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1427342011072 L-aspartate oxidase; Provisional; Region: PRK06175 1427342011073 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK05675 1427342011074 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1427342011075 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 1427342011076 SdhC subunit interface [polypeptide binding]; other site 1427342011077 proximal heme binding site [chemical binding]; other site 1427342011078 cardiolipin binding site; other site 1427342011079 Iron-sulfur protein interface; other site 1427342011080 proximal quinone binding site [chemical binding]; other site 1427342011081 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 1427342011082 SdhD (CybS) interface [polypeptide binding]; other site 1427342011083 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 1427342011084 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1427342011085 dimer interface [polypeptide binding]; other site 1427342011086 active site 1427342011087 citrylCoA binding site [chemical binding]; other site 1427342011088 NADH binding [chemical binding]; other site 1427342011089 cationic pore residues; other site 1427342011090 oxalacetate/citrate binding site [chemical binding]; other site 1427342011091 coenzyme A binding site [chemical binding]; other site 1427342011092 catalytic triad [active] 1427342011093 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family; Region: START_1; cd08876 1427342011094 putative lipid binding site [chemical binding]; other site 1427342011095 Protein of unknown function, DUF486; Region: DUF486; pfam04342 1427342011096 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 1427342011097 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1427342011098 DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; Region: ERI-1_3'hExo_like; cd06133 1427342011099 active site 1427342011100 catalytic site [active] 1427342011101 substrate binding site [chemical binding]; other site 1427342011102 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 1427342011103 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3738 1427342011104 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 1427342011105 ATP-NAD kinase; Region: NAD_kinase; pfam01513 1427342011106 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 1427342011107 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011108 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342011109 dimerization interface [polypeptide binding]; other site 1427342011110 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1427342011111 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011112 putative substrate translocation pore; other site 1427342011113 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011114 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 1427342011115 homotrimer interaction site [polypeptide binding]; other site 1427342011116 putative active site [active] 1427342011117 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342011118 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342011119 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342011120 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342011121 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342011122 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342011123 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 1427342011124 CPxP motif; other site 1427342011125 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 1427342011126 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1427342011127 aconitate hydratase; Validated; Region: PRK09277 1427342011128 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1427342011129 substrate binding site [chemical binding]; other site 1427342011130 ligand binding site [chemical binding]; other site 1427342011131 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 1427342011132 substrate binding site [chemical binding]; other site 1427342011133 PAS domain; Region: PAS_9; pfam13426 1427342011134 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342011135 putative active site [active] 1427342011136 heme pocket [chemical binding]; other site 1427342011137 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342011138 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342011139 dimer interface [polypeptide binding]; other site 1427342011140 putative CheW interface [polypeptide binding]; other site 1427342011141 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342011142 NAD(P) binding site [chemical binding]; other site 1427342011143 active site 1427342011144 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 1427342011145 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 1427342011146 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 1427342011147 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1427342011148 Low-spin heme binding site [chemical binding]; other site 1427342011149 Putative water exit pathway; other site 1427342011150 Binuclear center (active site) [active] 1427342011151 Putative proton exit pathway; other site 1427342011152 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 1427342011153 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 1427342011154 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 1427342011155 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 1427342011156 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342011157 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342011158 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 1427342011159 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1427342011160 Low-spin heme binding site [chemical binding]; other site 1427342011161 Putative water exit pathway; other site 1427342011162 Binuclear center (active site) [active] 1427342011163 Putative proton exit pathway; other site 1427342011164 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 1427342011165 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 1427342011166 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 1427342011167 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 1427342011168 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1427342011169 Cytochrome c; Region: Cytochrom_C; cl11414 1427342011170 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 1427342011171 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1427342011172 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 1427342011173 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 1427342011174 FixH; Region: FixH; pfam05751 1427342011175 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 1427342011176 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1427342011177 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 1427342011178 metal-binding site [ion binding] 1427342011179 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342011180 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342011181 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 1427342011182 Uncharacterized conserved protein [Function unknown]; Region: COG2836 1427342011183 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 1427342011184 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342011185 FeS/SAM binding site; other site 1427342011186 HemN C-terminal domain; Region: HemN_C; pfam06969 1427342011187 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 1427342011188 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342011189 ligand binding site [chemical binding]; other site 1427342011190 flexible hinge region; other site 1427342011191 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 1427342011192 putative switch regulator; other site 1427342011193 non-specific DNA interactions [nucleotide binding]; other site 1427342011194 DNA binding site [nucleotide binding] 1427342011195 sequence specific DNA binding site [nucleotide binding]; other site 1427342011196 putative cAMP binding site [chemical binding]; other site 1427342011197 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342011198 active site 1427342011199 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 1427342011200 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 1427342011201 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 1427342011202 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 1427342011203 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011204 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 1427342011205 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 1427342011206 short chain dehydrogenase; Provisional; Region: PRK06181 1427342011207 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342011208 NAD(P) binding site [chemical binding]; other site 1427342011209 active site 1427342011210 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3196 1427342011211 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342011212 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342011213 active site 1427342011214 recombination protein RecR; Reviewed; Region: recR; PRK00076 1427342011215 RecR protein; Region: RecR; pfam02132 1427342011216 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 1427342011217 putative active site [active] 1427342011218 putative metal-binding site [ion binding]; other site 1427342011219 tetramer interface [polypeptide binding]; other site 1427342011220 hypothetical protein; Validated; Region: PRK00153 1427342011221 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 1427342011222 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342011223 Walker A motif; other site 1427342011224 ATP binding site [chemical binding]; other site 1427342011225 Walker B motif; other site 1427342011226 arginine finger; other site 1427342011227 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1427342011228 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342011229 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342011230 substrate binding pocket [chemical binding]; other site 1427342011231 membrane-bound complex binding site; other site 1427342011232 hinge residues; other site 1427342011233 Ligase N family; Region: LIGANc; smart00532 1427342011234 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 1427342011235 nucleotide binding pocket [chemical binding]; other site 1427342011236 K-X-D-G motif; other site 1427342011237 catalytic site [active] 1427342011238 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1427342011239 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1427342011240 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 1427342011241 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 1427342011242 Dimer interface [polypeptide binding]; other site 1427342011243 BRCT sequence motif; other site 1427342011244 Cell division protein [Cell division and chromosome partitioning]; Region: ZipA; COG3115 1427342011245 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cd00231 1427342011246 FtsZ protein binding site [polypeptide binding]; other site 1427342011247 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1427342011248 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1427342011249 Walker A/P-loop; other site 1427342011250 ATP binding site [chemical binding]; other site 1427342011251 Q-loop/lid; other site 1427342011252 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 1427342011253 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1427342011254 ABC transporter signature motif; other site 1427342011255 Walker B; other site 1427342011256 D-loop; other site 1427342011257 H-loop/switch region; other site 1427342011258 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342011259 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342011260 DNA-binding site [nucleotide binding]; DNA binding site 1427342011261 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 1427342011262 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 1427342011263 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1427342011264 Di-iron ligands [ion binding]; other site 1427342011265 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 1427342011266 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342011267 catalytic loop [active] 1427342011268 iron binding site [ion binding]; other site 1427342011269 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342011270 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 1427342011271 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 1427342011272 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1427342011273 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342011274 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 1427342011275 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 1427342011276 XdhC Rossmann domain; Region: XdhC_C; pfam13478 1427342011277 guanine deaminase; Provisional; Region: PRK09228 1427342011278 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 1427342011279 active site 1427342011280 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342011281 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342011282 DNA-binding site [nucleotide binding]; DNA binding site 1427342011283 FCD domain; Region: FCD; pfam07729 1427342011284 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1427342011285 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1427342011286 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 1427342011287 active site 1427342011288 homotetramer interface [polypeptide binding]; other site 1427342011289 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 1427342011290 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 1427342011291 active site 1427342011292 catalytic site [active] 1427342011293 tetramer interface [polypeptide binding]; other site 1427342011294 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3195 1427342011295 Allantoicase [Nucleotide transport and metabolism]; Region: Alc; COG4266 1427342011296 Allantoicase repeat; Region: Allantoicase; pfam03561 1427342011297 Allantoicase repeat; Region: Allantoicase; pfam03561 1427342011298 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 1427342011299 ureidoglycolate hydrolase; Provisional; Region: PRK03606 1427342011300 Predicted membrane protein [Function unknown]; Region: COG3748 1427342011301 Protein of unknown function (DUF989); Region: DUF989; pfam06181 1427342011302 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342011303 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 1427342011304 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 1427342011305 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342011306 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342011307 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 1427342011308 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 1427342011309 PGAP1-like protein; Region: PGAP1; pfam07819 1427342011310 PAAR motif; Region: PAAR_motif; pfam05488 1427342011311 xanthine permease; Region: pbuX; TIGR03173 1427342011312 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG4551 1427342011313 active site 1427342011314 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 1427342011315 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342011316 FeS/SAM binding site; other site 1427342011317 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 1427342011318 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 1427342011319 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011320 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 1427342011321 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 1427342011322 glyoxylate carboligase; Provisional; Region: PRK11269 1427342011323 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342011324 PYR/PP interface [polypeptide binding]; other site 1427342011325 dimer interface [polypeptide binding]; other site 1427342011326 TPP binding site [chemical binding]; other site 1427342011327 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342011328 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1427342011329 TPP-binding site [chemical binding]; other site 1427342011330 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 1427342011331 tartronate semialdehyde reductase; Provisional; Region: PRK15059 1427342011332 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1427342011333 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 1427342011334 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 1427342011335 MOFRL family; Region: MOFRL; pfam05161 1427342011336 pyruvate kinase; Provisional; Region: PRK06247 1427342011337 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 1427342011338 domain interfaces; other site 1427342011339 active site 1427342011340 Urea transporter [Amino acid transport and metabolism]; Region: Utp; COG4413 1427342011341 Ion transport protein; Region: Ion_trans; pfam00520 1427342011342 Ion channel; Region: Ion_trans_2; pfam07885 1427342011343 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4339 1427342011344 conserved hypothetical protein; Region: TIGR02231 1427342011345 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 1427342011346 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 1427342011347 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 1427342011348 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 1427342011349 Domain of unknown function (DUF1937); Region: DUF1937; pfam09152 1427342011350 Ethanolamine utilization protein [Amino acid transport and metabolism]; Region: EutH; COG3192 1427342011351 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 1427342011352 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 1427342011353 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 1427342011354 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1427342011355 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342011356 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1427342011357 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 1427342011358 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342011359 Proteobacterial glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_GK_like_proteobact; cd07794 1427342011360 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 1427342011361 N- and C-terminal domain interface [polypeptide binding]; other site 1427342011362 active site 1427342011363 MgATP binding site [chemical binding]; other site 1427342011364 catalytic site [active] 1427342011365 metal binding site [ion binding]; metal-binding site 1427342011366 putative homotetramer interface [polypeptide binding]; other site 1427342011367 putative homodimer interface [polypeptide binding]; other site 1427342011368 putative glycerol binding site [chemical binding]; other site 1427342011369 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 1427342011370 homodimer interface [polypeptide binding]; other site 1427342011371 homotetramer interface [polypeptide binding]; other site 1427342011372 active site pocket [active] 1427342011373 cleavage site 1427342011374 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342011375 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342011376 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342011377 DNA binding residues [nucleotide binding] 1427342011378 dimerization interface [polypeptide binding]; other site 1427342011379 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 1427342011380 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 1427342011381 Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]; Region: CcmH; COG3088 1427342011382 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 1427342011383 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 1427342011384 catalytic residues [active] 1427342011385 central insert; other site 1427342011386 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1427342011387 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1427342011388 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 1427342011389 heme exporter protein CcmC; Region: ccmC; TIGR01191 1427342011390 heme exporter protein CcmB; Region: ccmB; TIGR01190 1427342011391 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 1427342011392 Cytochrome c biogenesis ATP-binding export protein; Region: ABC_CcmA_heme_exporter; cd03231 1427342011393 Walker A/P-loop; other site 1427342011394 ATP binding site [chemical binding]; other site 1427342011395 Q-loop/lid; other site 1427342011396 ABC transporter signature motif; other site 1427342011397 Walker B; other site 1427342011398 D-loop; other site 1427342011399 H-loop/switch region; other site 1427342011400 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 1427342011401 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 1427342011402 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 1427342011403 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342011404 short chain dehydrogenase; Provisional; Region: PRK12937 1427342011405 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 1427342011406 NADP binding site [chemical binding]; other site 1427342011407 homodimer interface [polypeptide binding]; other site 1427342011408 active site 1427342011409 substrate binding site [chemical binding]; other site 1427342011410 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 1427342011411 Predicted transcriptional regulator [Transcription]; Region: COG2378 1427342011412 HTH domain; Region: HTH_11; pfam08279 1427342011413 WYL domain; Region: WYL; pfam13280 1427342011414 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 1427342011415 C-terminal domain interface [polypeptide binding]; other site 1427342011416 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342011417 GSH binding site (G-site) [chemical binding]; other site 1427342011418 dimer interface [polypeptide binding]; other site 1427342011419 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 1427342011420 N-terminal domain interface [polypeptide binding]; other site 1427342011421 dimer interface [polypeptide binding]; other site 1427342011422 substrate binding pocket (H-site) [chemical binding]; other site 1427342011423 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 1427342011424 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 1427342011425 putative CheA interaction surface; other site 1427342011426 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 1427342011427 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1427342011428 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342011429 P-loop; other site 1427342011430 Magnesium ion binding site [ion binding]; other site 1427342011431 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342011432 Magnesium ion binding site [ion binding]; other site 1427342011433 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 1427342011434 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 1427342011435 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342011436 ligand binding site [chemical binding]; other site 1427342011437 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 1427342011438 flagellar motor protein; Reviewed; Region: motC; PRK09109 1427342011439 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 1427342011440 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011441 active site 1427342011442 phosphorylation site [posttranslational modification] 1427342011443 intermolecular recognition site; other site 1427342011444 dimerization interface [polypeptide binding]; other site 1427342011445 CheB methylesterase; Region: CheB_methylest; pfam01339 1427342011446 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342011447 putative binding surface; other site 1427342011448 active site 1427342011449 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1427342011450 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1427342011451 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342011452 ATP binding site [chemical binding]; other site 1427342011453 Mg2+ binding site [ion binding]; other site 1427342011454 G-X-G motif; other site 1427342011455 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 1427342011456 Chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheZ; COG3143 1427342011457 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 1427342011458 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011459 active site 1427342011460 phosphorylation site [posttranslational modification] 1427342011461 intermolecular recognition site; other site 1427342011462 dimerization interface [polypeptide binding]; other site 1427342011463 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 1427342011464 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342011465 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1427342011466 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342011467 DNA binding residues [nucleotide binding] 1427342011468 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 1427342011469 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 1427342011470 P-loop; other site 1427342011471 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 1427342011472 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 1427342011473 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 1427342011474 FHIPEP family; Region: FHIPEP; pfam00771 1427342011475 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 1427342011476 Repair protein; Region: Repair_PSII; pfam04536 1427342011477 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 1427342011478 Repair protein; Region: Repair_PSII; pfam04536 1427342011479 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 1427342011480 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 1427342011481 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 1427342011482 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 1427342011483 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 1427342011484 Flagellar biogenesis protein [Cell motility and secretion]; Region: FliO; COG3190 1427342011485 flagellar motor switch protein; Validated; Region: fliN; PRK05698 1427342011486 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 1427342011487 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 1427342011488 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 1427342011489 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 1427342011490 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 1427342011491 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 1427342011492 Predicted metal-binding protein related to the C-terminal domain of SecA [General function prediction only]; Region: COG3318 1427342011493 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 1427342011494 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 1427342011495 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 1427342011496 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342011497 dimer interface [polypeptide binding]; other site 1427342011498 phosphorylation site [posttranslational modification] 1427342011499 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342011500 ATP binding site [chemical binding]; other site 1427342011501 Mg2+ binding site [ion binding]; other site 1427342011502 G-X-G motif; other site 1427342011503 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 1427342011504 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011505 active site 1427342011506 phosphorylation site [posttranslational modification] 1427342011507 intermolecular recognition site; other site 1427342011508 dimerization interface [polypeptide binding]; other site 1427342011509 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342011510 DNA binding site [nucleotide binding] 1427342011511 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1427342011512 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342011513 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342011514 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342011515 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 1427342011516 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342011517 metal binding site [ion binding]; metal-binding site 1427342011518 active site 1427342011519 I-site; other site 1427342011520 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342011521 N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: LasI; COG3916 1427342011522 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342011523 DNA binding residues [nucleotide binding] 1427342011524 dimerization interface [polypeptide binding]; other site 1427342011525 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 1427342011526 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 1427342011527 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342011528 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 1427342011529 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1427342011530 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 1427342011531 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1427342011532 FOG: WD40 repeat [General function prediction only]; Region: COG2319 1427342011533 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 1427342011534 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1427342011535 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342011536 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342011537 Walker A/P-loop; other site 1427342011538 Walker A/P-loop; other site 1427342011539 ATP binding site [chemical binding]; other site 1427342011540 ATP binding site [chemical binding]; other site 1427342011541 Q-loop/lid; other site 1427342011542 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342011543 Q-loop/lid; other site 1427342011544 ABC transporter signature motif; other site 1427342011545 ABC transporter signature motif; other site 1427342011546 Walker B; other site 1427342011547 Walker B; other site 1427342011548 D-loop; other site 1427342011549 H-loop/switch region; other site 1427342011550 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342011551 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 1427342011552 Uncharacterized conserved protein [Function unknown]; Region: COG3148 1427342011553 PAS domain; Region: PAS_9; pfam13426 1427342011554 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342011555 putative active site [active] 1427342011556 heme pocket [chemical binding]; other site 1427342011557 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342011558 PAS domain; Region: PAS_9; pfam13426 1427342011559 putative active site [active] 1427342011560 heme pocket [chemical binding]; other site 1427342011561 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342011562 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342011563 dimer interface [polypeptide binding]; other site 1427342011564 putative CheW interface [polypeptide binding]; other site 1427342011565 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011566 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011567 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342011568 dimerization interface [polypeptide binding]; other site 1427342011569 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 1427342011570 agmatinase; Region: agmatinase; TIGR01230 1427342011571 oligomer interface [polypeptide binding]; other site 1427342011572 putative active site [active] 1427342011573 Mn binding site [ion binding]; other site 1427342011574 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 1427342011575 SnoaL-like domain; Region: SnoaL_3; pfam13474 1427342011576 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 1427342011577 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342011578 Na binding site [ion binding]; other site 1427342011579 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u3; cd11479 1427342011580 Na binding site [ion binding]; other site 1427342011581 hypothetical protein; Provisional; Region: PRK07524 1427342011582 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342011583 PYR/PP interface [polypeptide binding]; other site 1427342011584 dimer interface [polypeptide binding]; other site 1427342011585 TPP binding site [chemical binding]; other site 1427342011586 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342011587 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 1427342011588 TPP-binding site [chemical binding]; other site 1427342011589 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1427342011590 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342011591 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342011592 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011593 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011594 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 1427342011595 putative dimerization interface [polypeptide binding]; other site 1427342011596 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 1427342011597 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1427342011598 EamA-like transporter family; Region: EamA; pfam00892 1427342011599 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342011600 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342011601 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 1427342011602 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 1427342011603 active site 1427342011604 Zn binding site [ion binding]; other site 1427342011605 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1427342011606 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 1427342011607 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342011608 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 1427342011609 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342011610 S-adenosylmethionine binding site [chemical binding]; other site 1427342011611 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1427342011612 active site 1427342011613 NTP binding site [chemical binding]; other site 1427342011614 metal binding triad [ion binding]; metal-binding site 1427342011615 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1427342011616 Family description; Region: UvrD_C_2; pfam13538 1427342011617 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342011618 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011619 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 1427342011620 Methyltransferase domain; Region: Methyltransf_24; pfam13578 1427342011621 Predicted ester cyclase [General function prediction only]; Region: COG5485 1427342011622 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1427342011623 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 1427342011624 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342011625 carboxyltransferase (CT) interaction site; other site 1427342011626 biotinylation site [posttranslational modification]; other site 1427342011627 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1427342011628 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1427342011629 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011630 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011631 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 1427342011632 substrate binding pocket [chemical binding]; other site 1427342011633 dimerization interface [polypeptide binding]; other site 1427342011634 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342011635 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011636 active site 1427342011637 phosphorylation site [posttranslational modification] 1427342011638 intermolecular recognition site; other site 1427342011639 dimerization interface [polypeptide binding]; other site 1427342011640 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342011641 DNA binding residues [nucleotide binding] 1427342011642 dimerization interface [polypeptide binding]; other site 1427342011643 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342011644 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342011645 dimer interface [polypeptide binding]; other site 1427342011646 phosphorylation site [posttranslational modification] 1427342011647 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 1427342011648 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342011649 ATP binding site [chemical binding]; other site 1427342011650 Mg2+ binding site [ion binding]; other site 1427342011651 G-X-G motif; other site 1427342011652 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342011653 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011654 active site 1427342011655 phosphorylation site [posttranslational modification] 1427342011656 intermolecular recognition site; other site 1427342011657 dimerization interface [polypeptide binding]; other site 1427342011658 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 1427342011659 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342011660 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342011661 short chain dehydrogenase; Provisional; Region: PRK06180 1427342011662 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1427342011663 NADP binding site [chemical binding]; other site 1427342011664 active site 1427342011665 steroid binding site; other site 1427342011666 putative acetyltransferase YhhY; Provisional; Region: PRK10140 1427342011667 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342011668 Coenzyme A binding pocket [chemical binding]; other site 1427342011669 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 1427342011670 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; pfam06315 1427342011671 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 1427342011672 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 1427342011673 ligand binding site [chemical binding]; other site 1427342011674 NAD binding site [chemical binding]; other site 1427342011675 catalytic site [active] 1427342011676 homodimer interface [polypeptide binding]; other site 1427342011677 Predicted transcriptional regulators [Transcription]; Region: COG1733 1427342011678 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 1427342011679 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 1427342011680 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 1427342011681 dimer interface [polypeptide binding]; other site 1427342011682 active site 1427342011683 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 1427342011684 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342011685 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342011686 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342011687 N-terminal plug; other site 1427342011688 ligand-binding site [chemical binding]; other site 1427342011689 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342011690 FecR protein; Region: FecR; pfam04773 1427342011691 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1427342011692 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342011693 DNA binding residues [nucleotide binding] 1427342011694 multidrug efflux protein; Reviewed; Region: PRK01766 1427342011695 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 1427342011696 cation binding site [ion binding]; other site 1427342011697 threonine and homoserine efflux system; Provisional; Region: PRK10532 1427342011698 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342011699 non-specific DNA binding site [nucleotide binding]; other site 1427342011700 salt bridge; other site 1427342011701 sequence-specific DNA binding site [nucleotide binding]; other site 1427342011702 Cupin domain; Region: Cupin_2; pfam07883 1427342011703 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 1427342011704 dimer interface [polypeptide binding]; other site 1427342011705 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 1427342011706 putative deacylase active site [active] 1427342011707 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 1427342011708 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342011709 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 1427342011710 dimer interface [polypeptide binding]; other site 1427342011711 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 1427342011712 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342011713 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 1427342011714 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4312 1427342011715 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 1427342011716 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342011717 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342011718 DNA binding residues [nucleotide binding] 1427342011719 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 1427342011720 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 1427342011721 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 1427342011722 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 1427342011723 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 1427342011724 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342011725 short chain dehydrogenase; Provisional; Region: PRK06523 1427342011726 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342011727 NAD(P) binding site [chemical binding]; other site 1427342011728 active site 1427342011729 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 1427342011730 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342011731 substrate binding pocket [chemical binding]; other site 1427342011732 membrane-bound complex binding site; other site 1427342011733 hinge residues; other site 1427342011734 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342011735 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342011736 dimer interface [polypeptide binding]; other site 1427342011737 conserved gate region; other site 1427342011738 putative PBP binding loops; other site 1427342011739 ABC-ATPase subunit interface; other site 1427342011740 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342011741 dimer interface [polypeptide binding]; other site 1427342011742 conserved gate region; other site 1427342011743 putative PBP binding loops; other site 1427342011744 ABC-ATPase subunit interface; other site 1427342011745 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342011746 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342011747 Walker A/P-loop; other site 1427342011748 ATP binding site [chemical binding]; other site 1427342011749 Q-loop/lid; other site 1427342011750 ABC transporter signature motif; other site 1427342011751 Walker B; other site 1427342011752 D-loop; other site 1427342011753 H-loop/switch region; other site 1427342011754 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 1427342011755 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 1427342011756 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 1427342011757 homodimer interface [polypeptide binding]; other site 1427342011758 active site 1427342011759 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 1427342011760 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342011761 dimer interface [polypeptide binding]; other site 1427342011762 phosphorylation site [posttranslational modification] 1427342011763 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342011764 ATP binding site [chemical binding]; other site 1427342011765 Mg2+ binding site [ion binding]; other site 1427342011766 G-X-G motif; other site 1427342011767 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342011768 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342011769 active site 1427342011770 phosphorylation site [posttranslational modification] 1427342011771 intermolecular recognition site; other site 1427342011772 dimerization interface [polypeptide binding]; other site 1427342011773 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342011774 Walker A motif; other site 1427342011775 ATP binding site [chemical binding]; other site 1427342011776 Walker B motif; other site 1427342011777 arginine finger; other site 1427342011778 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342011779 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 1427342011780 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342011781 FMN binding site [chemical binding]; other site 1427342011782 active site 1427342011783 substrate binding site [chemical binding]; other site 1427342011784 catalytic residue [active] 1427342011785 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1427342011786 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342011787 S-adenosylmethionine binding site [chemical binding]; other site 1427342011788 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 1427342011789 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1427342011790 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 1427342011791 Transporter associated domain; Region: CorC_HlyC; smart01091 1427342011792 short chain dehydrogenase; Provisional; Region: PRK09291 1427342011793 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1427342011794 NADP binding site [chemical binding]; other site 1427342011795 active site 1427342011796 steroid binding site; other site 1427342011797 Domain of unknown function (DUF336); Region: DUF336; cl01249 1427342011798 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011799 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011800 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 1427342011801 putative effector binding pocket; other site 1427342011802 putative dimerization interface [polypeptide binding]; other site 1427342011803 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1427342011804 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 1427342011805 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 1427342011806 active site 1427342011807 substrate binding site [chemical binding]; other site 1427342011808 Mg2+ binding site [ion binding]; other site 1427342011809 threonine dehydratase; Reviewed; Region: PRK09224 1427342011810 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1427342011811 tetramer interface [polypeptide binding]; other site 1427342011812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342011813 catalytic residue [active] 1427342011814 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 1427342011815 putative Ile/Val binding site [chemical binding]; other site 1427342011816 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 1427342011817 putative Ile/Val binding site [chemical binding]; other site 1427342011818 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 1427342011819 Uncharacterized conserved protein [Function unknown]; Region: ElaB; COG4575 1427342011820 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 1427342011821 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342011822 N-terminal plug; other site 1427342011823 ligand-binding site [chemical binding]; other site 1427342011824 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 1427342011825 UbiA prenyltransferase family; Region: UbiA; pfam01040 1427342011826 Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]; Region: CyoD; COG3125 1427342011827 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 1427342011828 Subunit I/III interface [polypeptide binding]; other site 1427342011829 Subunit III/IV interface [polypeptide binding]; other site 1427342011830 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 1427342011831 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 1427342011832 D-pathway; other site 1427342011833 Putative ubiquinol binding site [chemical binding]; other site 1427342011834 Low-spin heme (heme b) binding site [chemical binding]; other site 1427342011835 Putative water exit pathway; other site 1427342011836 Binuclear center (heme o3/CuB) [ion binding]; other site 1427342011837 K-pathway; other site 1427342011838 Putative proton exit pathway; other site 1427342011839 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 1427342011840 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1427342011841 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 1427342011842 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342011843 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011844 putative substrate translocation pore; other site 1427342011845 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342011846 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011847 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4460 1427342011848 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011849 putative substrate translocation pore; other site 1427342011850 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011851 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011852 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011853 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342011854 putative effector binding pocket; other site 1427342011855 dimerization interface [polypeptide binding]; other site 1427342011856 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 1427342011857 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342011858 motif II; other site 1427342011859 2-aminoethylphosphonate--pyruvate transaminase; Provisional; Region: PRK13479 1427342011860 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342011861 catalytic residue [active] 1427342011862 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011863 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 1427342011864 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342011865 dimerization interface [polypeptide binding]; other site 1427342011866 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 1427342011867 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 1427342011868 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 1427342011869 putative active site [active] 1427342011870 putative dimer interface [polypeptide binding]; other site 1427342011871 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 1427342011872 nucleotide binding site/active site [active] 1427342011873 HIT family signature motif; other site 1427342011874 catalytic residue [active] 1427342011875 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1427342011876 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342011877 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1427342011878 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 1427342011879 Catalytic site [active] 1427342011880 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342011881 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 1427342011882 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342011883 N-terminal plug; other site 1427342011884 ligand-binding site [chemical binding]; other site 1427342011885 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342011886 FecR protein; Region: FecR; pfam04773 1427342011887 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1427342011888 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342011889 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 1427342011890 DNA binding residues [nucleotide binding] 1427342011891 hypothetical protein; Provisional; Region: PRK05170 1427342011892 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 1427342011893 putative metal binding site [ion binding]; other site 1427342011894 putative homodimer interface [polypeptide binding]; other site 1427342011895 putative homotetramer interface [polypeptide binding]; other site 1427342011896 putative homodimer-homodimer interface [polypeptide binding]; other site 1427342011897 putative allosteric switch controlling residues; other site 1427342011898 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 1427342011899 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 1427342011900 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 1427342011901 NAD binding site [chemical binding]; other site 1427342011902 ligand binding site [chemical binding]; other site 1427342011903 catalytic site [active] 1427342011904 YcgL domain; Region: YcgL; pfam05166 1427342011905 ribonuclease D; Region: rnd; TIGR01388 1427342011906 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1427342011907 catalytic site [active] 1427342011908 putative active site [active] 1427342011909 putative substrate binding site [chemical binding]; other site 1427342011910 HRDC domain; Region: HRDC; pfam00570 1427342011911 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 1427342011912 Strictosidine synthase; Region: Str_synth; pfam03088 1427342011913 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 1427342011914 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 1427342011915 active site residue [active] 1427342011916 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 1427342011917 active site residue [active] 1427342011918 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 1427342011919 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342011920 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011921 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 1427342011922 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 1427342011923 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342011924 catalytic residues [active] 1427342011925 dimer interface [polypeptide binding]; other site 1427342011926 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342011927 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011928 MarR family; Region: MarR_2; pfam12802 1427342011929 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342011930 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342011931 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342011932 active site 1427342011933 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342011934 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342011935 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342011936 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 1427342011937 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011938 cobalamin synthase; Reviewed; Region: cobS; PRK00235 1427342011939 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 1427342011940 catalytic core [active] 1427342011941 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 1427342011942 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 1427342011943 putative dimer interface [polypeptide binding]; other site 1427342011944 active site pocket [active] 1427342011945 putative cataytic base [active] 1427342011946 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 1427342011947 homotrimer interface [polypeptide binding]; other site 1427342011948 Walker A motif; other site 1427342011949 GTP binding site [chemical binding]; other site 1427342011950 Walker B motif; other site 1427342011951 cobyric acid synthase; Provisional; Region: PRK00784 1427342011952 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 1427342011953 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 1427342011954 catalytic triad [active] 1427342011955 threonine-phosphate decarboxylase; Reviewed; Region: PRK05664 1427342011956 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 1427342011957 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342011958 catalytic residue [active] 1427342011959 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 1427342011960 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 1427342011961 FMN binding site [chemical binding]; other site 1427342011962 dimer interface [polypeptide binding]; other site 1427342011963 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 1427342011964 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 1427342011965 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 1427342011966 catalytic triad [active] 1427342011967 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 1427342011968 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 1427342011969 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 1427342011970 homodimer interface [polypeptide binding]; other site 1427342011971 Walker A motif; other site 1427342011972 ATP binding site [chemical binding]; other site 1427342011973 hydroxycobalamin binding site [chemical binding]; other site 1427342011974 Walker B motif; other site 1427342011975 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 1427342011976 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342011977 N-terminal plug; other site 1427342011978 ligand-binding site [chemical binding]; other site 1427342011979 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342011980 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342011981 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342011982 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342011983 DNA-binding site [nucleotide binding]; DNA binding site 1427342011984 FCD domain; Region: FCD; pfam07729 1427342011985 hydroxyproline-2-epimerase; Provisional; Region: PRK13970 1427342011986 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 1427342011987 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342011988 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342011989 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 1427342011990 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342011991 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 1427342011992 EamA-like transporter family; Region: EamA; pfam00892 1427342011993 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342011994 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342011995 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342011996 Helix-turn-helix domain; Region: HTH_31; pfam13560 1427342011997 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342011998 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342011999 putative substrate translocation pore; other site 1427342012000 PAS fold; Region: PAS_4; pfam08448 1427342012001 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012002 putative active site [active] 1427342012003 heme pocket [chemical binding]; other site 1427342012004 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342012005 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342012006 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342012007 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342012008 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342012009 substrate binding pocket [chemical binding]; other site 1427342012010 membrane-bound complex binding site; other site 1427342012011 hinge residues; other site 1427342012012 Putative Aconitase X swivel domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure...; Region: AcnX_swivel; cd01356 1427342012013 substrate binding site [chemical binding]; other site 1427342012014 Protein of unknown function (DUF521); Region: DUF521; pfam04412 1427342012015 Putative Aconitase X catalytic domain; Region: AcnX; cd01355 1427342012016 substrate binding site [chemical binding]; other site 1427342012017 ligand binding site [chemical binding]; other site 1427342012018 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342012019 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342012020 dimer interface [polypeptide binding]; other site 1427342012021 conserved gate region; other site 1427342012022 putative PBP binding loops; other site 1427342012023 ABC-ATPase subunit interface; other site 1427342012024 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342012025 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342012026 dimer interface [polypeptide binding]; other site 1427342012027 conserved gate region; other site 1427342012028 putative PBP binding loops; other site 1427342012029 ABC-ATPase subunit interface; other site 1427342012030 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342012031 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342012032 Walker A/P-loop; other site 1427342012033 ATP binding site [chemical binding]; other site 1427342012034 Q-loop/lid; other site 1427342012035 ABC transporter signature motif; other site 1427342012036 Walker B; other site 1427342012037 D-loop; other site 1427342012038 H-loop/switch region; other site 1427342012039 Proline racemase [Amino acid transport and metabolism]; Region: COG3938 1427342012040 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 1427342012041 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 1427342012042 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 1427342012043 inhibitor site; inhibition site 1427342012044 active site 1427342012045 dimer interface [polypeptide binding]; other site 1427342012046 catalytic residue [active] 1427342012047 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1427342012048 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 1427342012049 dimer interface [polypeptide binding]; other site 1427342012050 NADP binding site [chemical binding]; other site 1427342012051 catalytic residues [active] 1427342012052 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 1427342012053 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1427342012054 HAMP domain; Region: HAMP; pfam00672 1427342012055 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342012056 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342012057 dimer interface [polypeptide binding]; other site 1427342012058 putative CheW interface [polypeptide binding]; other site 1427342012059 Protease inhibitor Inh; Region: Inh; pfam02974 1427342012060 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 1427342012061 active site 1427342012062 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 1427342012063 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 1427342012064 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1427342012065 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342012066 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342012067 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1427342012068 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342012069 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342012070 Walker A/P-loop; other site 1427342012071 ATP binding site [chemical binding]; other site 1427342012072 Q-loop/lid; other site 1427342012073 ABC transporter signature motif; other site 1427342012074 Walker B; other site 1427342012075 D-loop; other site 1427342012076 H-loop/switch region; other site 1427342012077 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 1427342012078 GAF domain; Region: GAF; pfam01590 1427342012079 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012080 PAS domain; Region: PAS_9; pfam13426 1427342012081 putative active site [active] 1427342012082 heme pocket [chemical binding]; other site 1427342012083 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342012084 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342012085 dimer interface [polypeptide binding]; other site 1427342012086 phosphorylation site [posttranslational modification] 1427342012087 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342012088 ATP binding site [chemical binding]; other site 1427342012089 Mg2+ binding site [ion binding]; other site 1427342012090 G-X-G motif; other site 1427342012091 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342012092 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342012093 active site 1427342012094 phosphorylation site [posttranslational modification] 1427342012095 intermolecular recognition site; other site 1427342012096 dimerization interface [polypeptide binding]; other site 1427342012097 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 1427342012098 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cd00306 1427342012099 active site 1427342012100 catalytic residues [active] 1427342012101 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342012102 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342012103 enoyl-CoA hydratase; Provisional; Region: PRK06563 1427342012104 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342012105 substrate binding site [chemical binding]; other site 1427342012106 oxyanion hole (OAH) forming residues; other site 1427342012107 trimer interface [polypeptide binding]; other site 1427342012108 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 1427342012109 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342012110 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1427342012111 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342012112 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342012113 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012114 putative substrate translocation pore; other site 1427342012115 Cupin domain; Region: Cupin_2; pfam07883 1427342012116 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342012117 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342012118 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342012119 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342012120 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342012121 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 1427342012122 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342012123 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342012124 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342012125 Phosphotransferase enzyme family; Region: APH; pfam01636 1427342012126 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342012127 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342012128 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1427342012129 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342012130 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 1427342012131 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 1427342012132 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 1427342012133 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342012134 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 1427342012135 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 1427342012136 putative active site; other site 1427342012137 catalytic triad [active] 1427342012138 putative dimer interface [polypeptide binding]; other site 1427342012139 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 1427342012140 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 1427342012141 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342012142 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012143 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 1427342012144 dimerization interface [polypeptide binding]; other site 1427342012145 substrate binding pocket [chemical binding]; other site 1427342012146 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 1427342012147 MltA specific insert domain; Region: MltA; pfam03562 1427342012148 3D domain; Region: 3D; pfam06725 1427342012149 The adenylation domain of nonribosomal peptide synthetases (NRPS), including Bacillus subtilis termination module Surfactin (SrfA-C); Region: A_NRPS_Srf_like; cd12117 1427342012150 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 1427342012151 acyl-activating enzyme (AAE) consensus motif; other site 1427342012152 AMP binding site [chemical binding]; other site 1427342012153 Thioesterase domain; Region: Thioesterase; pfam00975 1427342012154 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 1427342012155 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 1427342012156 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 1427342012157 active site 1427342012158 catalytic residues [active] 1427342012159 metal binding site [ion binding]; metal-binding site 1427342012160 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342012161 S-adenosylmethionine binding site [chemical binding]; other site 1427342012162 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 1427342012163 Adenylate forming domain, Class I; Region: AFD_class_I; cd04433 1427342012164 acyl-activating enzyme (AAE) consensus motif; other site 1427342012165 AMP binding site [chemical binding]; other site 1427342012166 active site 1427342012167 CoA binding site [chemical binding]; other site 1427342012168 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 1427342012169 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 1427342012170 active site 1427342012171 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 1427342012172 Ligand Binding Site [chemical binding]; other site 1427342012173 Molecular Tunnel; other site 1427342012174 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cd00250 1427342012175 substrate binding pocket [chemical binding]; other site 1427342012176 active site 1427342012177 iron coordination sites [ion binding]; other site 1427342012178 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012179 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342012180 putative substrate translocation pore; other site 1427342012181 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 1427342012182 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342012183 Pirin-related protein [General function prediction only]; Region: COG1741 1427342012184 Pirin; Region: Pirin; pfam02678 1427342012185 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1427342012186 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1427342012187 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1427342012188 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 1427342012189 active site residue [active] 1427342012190 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 1427342012191 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 1427342012192 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1427342012193 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 1427342012194 TrkA-N domain; Region: TrkA_N; pfam02254 1427342012195 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 1427342012196 putative hydrophobic ligand binding site [chemical binding]; other site 1427342012197 Pirin-related protein [General function prediction only]; Region: COG1741 1427342012198 Pirin; Region: Pirin; pfam02678 1427342012199 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1427342012200 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342012201 Predicted flavoprotein [General function prediction only]; Region: COG0431 1427342012202 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 1427342012203 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342012204 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1427342012205 catalytic triad [active] 1427342012206 dimer interface [polypeptide binding]; other site 1427342012207 conserved cis-peptide bond; other site 1427342012208 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012209 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012210 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342012211 putative effector binding pocket; other site 1427342012212 dimerization interface [polypeptide binding]; other site 1427342012213 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 1427342012214 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342012215 S-adenosylmethionine binding site [chemical binding]; other site 1427342012216 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1427342012217 NlpC/P60 family; Region: NLPC_P60; pfam00877 1427342012218 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1427342012219 NlpC/P60 family; Region: NLPC_P60; pfam00877 1427342012220 NAD-dependent deacetylase; Provisional; Region: PRK00481 1427342012221 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 1427342012222 NAD+ binding site [chemical binding]; other site 1427342012223 substrate binding site [chemical binding]; other site 1427342012224 Zn binding site [ion binding]; other site 1427342012225 photoactive yellow protein; Region: photo_yellow; TIGR02373 1427342012226 PAS domain; Region: PAS_9; pfam13426 1427342012227 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1427342012228 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342012229 Walker A motif; other site 1427342012230 ATP binding site [chemical binding]; other site 1427342012231 Walker B motif; other site 1427342012232 arginine finger; other site 1427342012233 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1427342012234 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 1427342012235 Amidinotransferase; Region: Amidinotransf; cl12043 1427342012236 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 1427342012237 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]; Region: Tag; COG2818 1427342012238 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 1427342012239 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 1427342012240 Ligand Binding Site [chemical binding]; other site 1427342012241 DNA-J related protein; Region: DNAJ_related; pfam12339 1427342012242 DnaJ molecular chaperone homology domain; Region: DnaJ; smart00271 1427342012243 HSP70 interaction site [polypeptide binding]; other site 1427342012244 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 1427342012245 hypothetical protein; Provisional; Region: PRK04860 1427342012246 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 1427342012247 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1427342012248 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1427342012249 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342012250 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342012251 active site 1427342012252 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 1427342012253 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 1427342012254 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 1427342012255 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 1427342012256 C-terminal domain interface [polypeptide binding]; other site 1427342012257 GSH binding site (G-site) [chemical binding]; other site 1427342012258 dimer interface [polypeptide binding]; other site 1427342012259 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 1427342012260 dimer interface [polypeptide binding]; other site 1427342012261 N-terminal domain interface [polypeptide binding]; other site 1427342012262 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342012263 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012264 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 1427342012265 dimerization interface [polypeptide binding]; other site 1427342012266 substrate binding pocket [chemical binding]; other site 1427342012267 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 1427342012268 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1427342012269 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342012270 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342012271 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342012272 Predicted integral membrane sensor domain [Signal transduction mechanisms]; Region: COG3447 1427342012273 putative diguanylate cyclase; Provisional; Region: PRK09776 1427342012274 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012275 putative active site [active] 1427342012276 heme pocket [chemical binding]; other site 1427342012277 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012278 putative active site [active] 1427342012279 heme pocket [chemical binding]; other site 1427342012280 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012281 putative active site [active] 1427342012282 heme pocket [chemical binding]; other site 1427342012283 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342012284 metal binding site [ion binding]; metal-binding site 1427342012285 active site 1427342012286 I-site; other site 1427342012287 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342012288 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342012289 dimer interface [polypeptide binding]; other site 1427342012290 phosphorylation site [posttranslational modification] 1427342012291 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342012292 ATP binding site [chemical binding]; other site 1427342012293 G-X-G motif; other site 1427342012294 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 1427342012295 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342012296 active site 1427342012297 phosphorylation site [posttranslational modification] 1427342012298 intermolecular recognition site; other site 1427342012299 dimerization interface [polypeptide binding]; other site 1427342012300 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342012301 DNA binding site [nucleotide binding] 1427342012302 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 1427342012303 Periplasmic nitrate reductase system, NapE component [Energy production and conversion]; Region: NapE; COG4459 1427342012304 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1427342012305 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1427342012306 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1427342012307 Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]; Region: NapD; COG3062 1427342012308 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 1427342012309 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 1427342012310 [4Fe-4S] binding site [ion binding]; other site 1427342012311 molybdopterin cofactor binding site; other site 1427342012312 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 1427342012313 molybdopterin cofactor binding site; other site 1427342012314 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 1427342012315 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 1427342012316 Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit [Energy production and conversion]; Region: TorC; COG3005 1427342012317 Transglycosylase SLT domain; Region: SLT_2; pfam13406 1427342012318 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342012319 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342012320 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 1427342012321 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1427342012322 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 1427342012323 Lipoxygenase; Region: Lipoxygenase; pfam00305 1427342012324 Alginate lyase; Region: Alginate_lyase2; pfam08787 1427342012325 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 1427342012326 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342012327 Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntD; COG2977 1427342012328 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 1427342012329 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 1427342012330 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 1427342012331 putative ATP binding site [chemical binding]; other site 1427342012332 putative substrate interface [chemical binding]; other site 1427342012333 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 1427342012334 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342012335 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 1427342012336 active site 1427342012337 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1427342012338 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1427342012339 metal binding site [ion binding]; metal-binding site 1427342012340 dimer interface [polypeptide binding]; other site 1427342012341 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 1427342012342 Methyltransferase domain; Region: Methyltransf_11; pfam08241 1427342012343 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342012344 DNA-binding site [nucleotide binding]; DNA binding site 1427342012345 RNA-binding motif; other site 1427342012346 sensor protein RstB; Provisional; Region: PRK10604 1427342012347 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342012348 dimerization interface [polypeptide binding]; other site 1427342012349 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342012350 dimer interface [polypeptide binding]; other site 1427342012351 phosphorylation site [posttranslational modification] 1427342012352 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342012353 ATP binding site [chemical binding]; other site 1427342012354 Mg2+ binding site [ion binding]; other site 1427342012355 G-X-G motif; other site 1427342012356 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 1427342012357 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342012358 active site 1427342012359 phosphorylation site [posttranslational modification] 1427342012360 intermolecular recognition site; other site 1427342012361 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342012362 DNA binding site [nucleotide binding] 1427342012363 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 1427342012364 ATP cone domain; Region: ATP-cone; pfam03477 1427342012365 ATP cone domain; Region: ATP-cone; pfam03477 1427342012366 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1427342012367 active site 1427342012368 dimer interface [polypeptide binding]; other site 1427342012369 catalytic residues [active] 1427342012370 effector binding site; other site 1427342012371 R2 peptide binding site; other site 1427342012372 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1427342012373 dimer interface [polypeptide binding]; other site 1427342012374 putative radical transfer pathway; other site 1427342012375 diiron center [ion binding]; other site 1427342012376 tyrosyl radical; other site 1427342012377 AAA domain; Region: AAA_22; pfam13401 1427342012378 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342012379 Walker A motif; other site 1427342012380 ATP binding site [chemical binding]; other site 1427342012381 Walker B motif; other site 1427342012382 BRO family, N-terminal domain; Region: Bro-N; cl10591 1427342012383 Colicin-like bacteriocin tRNase domain; Region: Cloacin; pfam03515 1427342012384 S-type Pyocin; Region: Pyocin_S; pfam06958 1427342012385 Colicin D; Region: Colicin_D; pfam11429 1427342012386 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 1427342012387 Exotoxin A binding; Region: Exotox-A_bind; pfam09101 1427342012388 Exotoxin A, targeting; Region: Exotox-A_target; pfam09102 1427342012389 Mono-ADP-ribosylating toxins catalyze the transfer of ADP_ribose from NAD+ to eukaryotic Elongation Factor 2, halting protein synthesis. A single molecule of delivered toxin is sufficient to kill a cell. These toxins share mono-ADP-ribosylating activity...; Region: Dipth_tox_like; cd01436 1427342012390 nad+ binding pocket [chemical binding]; other site 1427342012391 permease, urea carboxylase system; Region: ureacarb_perm; TIGR03428 1427342012392 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1427342012393 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 1427342012394 putative active site [active] 1427342012395 metal binding site [ion binding]; metal-binding site 1427342012396 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012397 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012398 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342012399 dimerization interface [polypeptide binding]; other site 1427342012400 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1427342012401 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012402 putative substrate translocation pore; other site 1427342012403 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 1427342012404 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342012405 transcriptional regulator protein; Region: phnR; TIGR03337 1427342012406 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342012407 DNA-binding site [nucleotide binding]; DNA binding site 1427342012408 UTRA domain; Region: UTRA; pfam07702 1427342012409 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 1427342012410 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 1427342012411 putative trimer interface [polypeptide binding]; other site 1427342012412 putative CoA binding site [chemical binding]; other site 1427342012413 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012414 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012415 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342012416 dimerization interface [polypeptide binding]; other site 1427342012417 hypothetical protein; Provisional; Region: PRK11171 1427342012418 Cupin domain; Region: Cupin_2; pfam07883 1427342012419 Cupin domain; Region: Cupin_2; pfam07883 1427342012420 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 1427342012421 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 1427342012422 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012423 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012424 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342012425 dimerization interface [polypeptide binding]; other site 1427342012426 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 1427342012427 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 1427342012428 NAD(P) binding site [chemical binding]; other site 1427342012429 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 1427342012430 Autoinducer binding domain; Region: Autoind_bind; pfam03472 1427342012431 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342012432 DNA binding residues [nucleotide binding] 1427342012433 dimerization interface [polypeptide binding]; other site 1427342012434 chaperone protein HchA; Provisional; Region: PRK04155 1427342012435 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 1427342012436 conserved cys residue [active] 1427342012437 Protein of unknown function, DUF393; Region: DUF393; cl01136 1427342012438 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012439 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342012440 RfbF is a putative dTDP-rhamnosyl transferase; Region: GT2_RfbF_like; cd02526 1427342012441 L-rhamnosyltransferase; Region: rhamnosyltran; TIGR01556 1427342012442 Ligand binding site; other site 1427342012443 FosA, a Fosfomycin resistance protein, catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive; Region: FosA; cd07244 1427342012444 dimer interface [polypeptide binding]; other site 1427342012445 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342012446 Mn binding site [ion binding]; other site 1427342012447 K binding site [ion binding]; other site 1427342012448 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012449 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012450 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 1427342012451 putative effector binding pocket; other site 1427342012452 putative dimerization interface [polypeptide binding]; other site 1427342012453 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342012454 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342012455 active site 1427342012456 catalytic tetrad [active] 1427342012457 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 1427342012458 NAD-dependent deacetylase; Provisional; Region: PRK00481 1427342012459 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 1427342012460 NAD+ binding site [chemical binding]; other site 1427342012461 substrate binding site [chemical binding]; other site 1427342012462 Zn binding site [ion binding]; other site 1427342012463 deoxyguanosinetriphosphate triphosphohydrolase; Provisional; Region: dgt; PRK04926 1427342012464 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342012465 Zn2+ binding site [ion binding]; other site 1427342012466 Mg2+ binding site [ion binding]; other site 1427342012467 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1427342012468 Protein of unknown function (DUF2025); Region: DUF2025; pfam09634 1427342012469 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 1427342012470 active site 1427342012471 catalytic residues [active] 1427342012472 metal binding site [ion binding]; metal-binding site 1427342012473 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 1427342012474 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 1427342012475 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342012476 dimerization interface [polypeptide binding]; other site 1427342012477 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342012478 metal binding site [ion binding]; metal-binding site 1427342012479 active site 1427342012480 I-site; other site 1427342012481 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342012482 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342012483 ligand binding site [chemical binding]; other site 1427342012484 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 1427342012485 S1 domain; Region: S1_2; pfam13509 1427342012486 S1 domain; Region: S1_2; pfam13509 1427342012487 Sulfatase; Region: Sulfatase; pfam00884 1427342012488 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 1427342012489 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1427342012490 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342012491 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342012492 Walker A/P-loop; other site 1427342012493 ATP binding site [chemical binding]; other site 1427342012494 Q-loop/lid; other site 1427342012495 ABC transporter signature motif; other site 1427342012496 Walker B; other site 1427342012497 D-loop; other site 1427342012498 H-loop/switch region; other site 1427342012499 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 1427342012500 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 1427342012501 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 1427342012502 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1427342012503 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342012504 RNA binding surface [nucleotide binding]; other site 1427342012505 Pseudouridine synthase, a subgroup of the RsuA family; Region: PSSA_1; cd02555 1427342012506 active site 1427342012507 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342012508 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342012509 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012510 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342012511 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342012512 metal binding site [ion binding]; metal-binding site 1427342012513 active site 1427342012514 I-site; other site 1427342012515 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 1427342012516 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 1427342012517 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 1427342012518 flagellum-specific ATP synthase; Validated; Region: fliI; PRK05688 1427342012519 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 1427342012520 Walker A motif/ATP binding site; other site 1427342012521 Walker B motif; other site 1427342012522 flagellar assembly protein H; Validated; Region: fliH; PRK05687 1427342012523 Flagellar assembly protein FliH; Region: FliH; pfam02108 1427342012524 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 1427342012525 MgtE intracellular N domain; Region: MgtE_N; smart00924 1427342012526 FliG C-terminal domain; Region: FliG_C; pfam01706 1427342012527 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 1427342012528 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 1427342012529 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 1427342012530 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 1427342012531 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342012532 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342012533 active site 1427342012534 phosphorylation site [posttranslational modification] 1427342012535 intermolecular recognition site; other site 1427342012536 dimerization interface [polypeptide binding]; other site 1427342012537 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342012538 Walker A motif; other site 1427342012539 ATP binding site [chemical binding]; other site 1427342012540 Walker B motif; other site 1427342012541 arginine finger; other site 1427342012542 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342012543 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342012544 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342012545 putative active site [active] 1427342012546 heme pocket [chemical binding]; other site 1427342012547 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342012548 dimer interface [polypeptide binding]; other site 1427342012549 phosphorylation site [posttranslational modification] 1427342012550 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342012551 ATP binding site [chemical binding]; other site 1427342012552 Mg2+ binding site [ion binding]; other site 1427342012553 G-X-G motif; other site 1427342012554 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342012555 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 1427342012556 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342012557 Walker A motif; other site 1427342012558 ATP binding site [chemical binding]; other site 1427342012559 Walker B motif; other site 1427342012560 arginine finger; other site 1427342012561 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342012562 flagellar protein FliS; Validated; Region: fliS; PRK05685 1427342012563 Flagellar protein FliS; Region: FliS; cl00654 1427342012564 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 1427342012565 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 1427342012566 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 1427342012567 FlaG protein; Region: FlaG; pfam03646 1427342012568 flagellin; Reviewed; Region: PRK08869 1427342012569 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1427342012570 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1427342012571 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1427342012572 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 1427342012573 active site 1427342012574 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342012575 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 1427342012576 active site 1427342012577 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 1427342012578 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 1427342012579 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 1427342012580 putative trimer interface [polypeptide binding]; other site 1427342012581 putative CoA binding site [chemical binding]; other site 1427342012582 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 1427342012583 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 1427342012584 [2Fe-2S] cluster binding site [ion binding]; other site 1427342012585 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 1427342012586 alpha subunit interface [polypeptide binding]; other site 1427342012587 active site 1427342012588 substrate binding site [chemical binding]; other site 1427342012589 Fe binding site [ion binding]; other site 1427342012590 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 1427342012591 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 1427342012592 putative trimer interface [polypeptide binding]; other site 1427342012593 putative CoA binding site [chemical binding]; other site 1427342012594 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342012595 classical (c) SDRs; Region: SDR_c; cd05233 1427342012596 NAD(P) binding site [chemical binding]; other site 1427342012597 active site 1427342012598 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 1427342012599 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 1427342012600 dimer interface [polypeptide binding]; other site 1427342012601 active site 1427342012602 CoA binding pocket [chemical binding]; other site 1427342012603 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 1427342012604 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1427342012605 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 1427342012606 inhibitor-cofactor binding pocket; inhibition site 1427342012607 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342012608 catalytic residue [active] 1427342012609 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 1427342012610 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1427342012611 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1427342012612 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK05683 1427342012613 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1427342012614 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 1427342012615 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 1427342012616 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 1427342012617 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 1427342012618 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 1427342012619 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 1427342012620 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 1427342012621 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 1427342012622 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1427342012623 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1427342012624 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 1427342012625 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1427342012626 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 1427342012627 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 1427342012628 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1427342012629 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 1427342012630 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1427342012631 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 1427342012632 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 1427342012633 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 1427342012634 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 1427342012635 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1427342012636 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1427342012637 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 1427342012638 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 1427342012639 Uncharacterized small conserved protein [Function unknown]; Region: COG5626 1427342012640 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1427342012641 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 1427342012642 dimerization interface [polypeptide binding]; other site 1427342012643 ligand binding site [chemical binding]; other site 1427342012644 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342012645 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 1427342012646 TM-ABC transporter signature motif; other site 1427342012647 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 1427342012648 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 1427342012649 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 1427342012650 TM-ABC transporter signature motif; other site 1427342012651 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 1427342012652 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 1427342012653 Walker A/P-loop; other site 1427342012654 ATP binding site [chemical binding]; other site 1427342012655 Q-loop/lid; other site 1427342012656 ABC transporter signature motif; other site 1427342012657 Walker B; other site 1427342012658 D-loop; other site 1427342012659 H-loop/switch region; other site 1427342012660 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 1427342012661 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 1427342012662 Walker A/P-loop; other site 1427342012663 ATP binding site [chemical binding]; other site 1427342012664 Q-loop/lid; other site 1427342012665 ABC transporter signature motif; other site 1427342012666 Walker B; other site 1427342012667 D-loop; other site 1427342012668 H-loop/switch region; other site 1427342012669 NMDA receptor-regulated protein 1; Region: NARP1; pfam12569 1427342012670 Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]; Region: HtpG; COG0326 1427342012671 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 1427342012672 ATP binding site [chemical binding]; other site 1427342012673 Mg2+ binding site [ion binding]; other site 1427342012674 G-X-G motif; other site 1427342012675 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012676 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012677 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342012678 putative effector binding pocket; other site 1427342012679 dimerization interface [polypeptide binding]; other site 1427342012680 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 1427342012681 putative NAD(P) binding site [chemical binding]; other site 1427342012682 homodimer interface [polypeptide binding]; other site 1427342012683 Uncharacterized conserved protein [Function unknown]; Region: COG3189 1427342012684 Predicted membrane protein [Function unknown]; Region: COG3650 1427342012685 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1427342012686 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1427342012687 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 1427342012688 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342012689 catalytic residue [active] 1427342012690 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1427342012691 EamA-like transporter family; Region: EamA; pfam00892 1427342012692 EamA-like transporter family; Region: EamA; pfam00892 1427342012693 Multisubunit Na+/H+ antiporter, MnhG subunit [Inorganic ion transport and metabolism]; Region: MnhG; COG1320 1427342012694 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 1427342012695 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 1427342012696 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 1427342012697 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1427342012698 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 1427342012699 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 1427342012700 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1427342012701 Domain of unknown function (DUF4040); Region: DUF4040; pfam13244 1427342012702 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12573 1427342012703 Outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]; Region: SlyB; COG3133 1427342012704 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 1427342012705 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 1427342012706 fructuronate transporter; Provisional; Region: PRK10034; cl15264 1427342012707 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 1427342012708 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 1427342012709 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1427342012710 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 1427342012711 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 1427342012712 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 1427342012713 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342012714 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342012715 ligand binding site [chemical binding]; other site 1427342012716 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342012717 Beta-lactamase; Region: Beta-lactamase; pfam00144 1427342012718 Beta-galactosidase; Region: Glyco_hydro_42; pfam02449 1427342012719 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 1427342012720 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 1427342012721 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 1427342012722 Predicted integral membrane protein [Function unknown]; Region: COG5615 1427342012723 Predicted membrane protein [Function unknown]; Region: COG3776 1427342012724 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342012725 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342012726 ligand binding site [chemical binding]; other site 1427342012727 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342012728 hypothetical protein; Provisional; Region: PRK00183 1427342012729 Predicted membrane protein [Function unknown]; Region: COG2860 1427342012730 UPF0126 domain; Region: UPF0126; pfam03458 1427342012731 UPF0126 domain; Region: UPF0126; pfam03458 1427342012732 LEA14-like dessication related protein [Defense mechanisms]; Region: COG5608 1427342012733 Water Stress and Hypersensitive response; Region: WHy; smart00769 1427342012734 SEC-C motif; Region: SEC-C; pfam02810 1427342012735 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 1427342012736 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 1427342012737 C-terminal domain interface [polypeptide binding]; other site 1427342012738 GSH binding site (G-site) [chemical binding]; other site 1427342012739 dimer interface [polypeptide binding]; other site 1427342012740 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 1427342012741 N-terminal domain interface [polypeptide binding]; other site 1427342012742 putative dimer interface [polypeptide binding]; other site 1427342012743 active site 1427342012744 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 1427342012745 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 1427342012746 active site 1427342012747 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1427342012748 RmuC family; Region: RmuC; pfam02646 1427342012749 RES domain; Region: RES; smart00953 1427342012750 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342012751 salt bridge; other site 1427342012752 sequence-specific DNA binding site [nucleotide binding]; other site 1427342012753 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 1427342012754 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342012755 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342012756 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1427342012757 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 1427342012758 tetrameric interface [polypeptide binding]; other site 1427342012759 NAD binding site [chemical binding]; other site 1427342012760 catalytic residues [active] 1427342012761 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1427342012762 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342012763 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 1427342012764 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 1427342012765 FMN binding site [chemical binding]; other site 1427342012766 substrate binding site [chemical binding]; other site 1427342012767 putative catalytic residue [active] 1427342012768 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 1427342012769 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342012770 NAD(P) binding site [chemical binding]; other site 1427342012771 active site 1427342012772 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 1427342012773 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342012774 active site 1427342012775 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 1427342012776 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342012777 substrate binding site [chemical binding]; other site 1427342012778 oxyanion hole (OAH) forming residues; other site 1427342012779 trimer interface [polypeptide binding]; other site 1427342012780 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 1427342012781 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342012782 active site 1427342012783 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342012784 CoenzymeA binding site [chemical binding]; other site 1427342012785 subunit interaction site [polypeptide binding]; other site 1427342012786 PHB binding site; other site 1427342012787 benzoate transport; Region: 2A0115; TIGR00895 1427342012788 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342012789 putative substrate translocation pore; other site 1427342012790 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 1427342012791 CoA binding domain; Region: CoA_binding_2; pfam13380 1427342012792 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 1427342012793 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 1427342012794 thiolase; Provisional; Region: PRK06158 1427342012795 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 1427342012796 active site 1427342012797 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 1427342012798 DUF35 OB-fold domain; Region: DUF35; pfam01796 1427342012799 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 1427342012800 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342012801 Bacterial transcriptional regulator; Region: IclR; pfam01614 1427342012802 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1427342012803 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 1427342012804 active site 1427342012805 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1427342012806 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1427342012807 ATP binding site [chemical binding]; other site 1427342012808 active site 1427342012809 substrate binding site [chemical binding]; other site 1427342012810 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1427342012811 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 1427342012812 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 1427342012813 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1427342012814 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1427342012815 dimer interface [polypeptide binding]; other site 1427342012816 active site 1427342012817 catalytic residue [active] 1427342012818 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 1427342012819 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 1427342012820 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 1427342012821 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1427342012822 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 1427342012823 catalytic triad [active] 1427342012824 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1427342012825 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1427342012826 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 1427342012827 CPxP motif; other site 1427342012828 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 1427342012829 Peptidase family M48; Region: Peptidase_M48; cl12018 1427342012830 quinolinate synthetase; Provisional; Region: PRK09375 1427342012831 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342012832 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342012833 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342012834 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1427342012835 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1427342012836 glutamine binding [chemical binding]; other site 1427342012837 catalytic triad [active] 1427342012838 anthranilate synthase component I; Provisional; Region: PRK13564 1427342012839 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 1427342012840 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1427342012841 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342012842 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 1427342012843 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 1427342012844 dimer interface [polypeptide binding]; other site 1427342012845 active site 1427342012846 CoA binding pocket [chemical binding]; other site 1427342012847 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 1427342012848 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 1427342012849 active site 1427342012850 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 1427342012851 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 1427342012852 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 1427342012853 Benzoate CoA ligase (BCL) and similar adenylate forming enzymes; Region: BCL_like; cd05919 1427342012854 dimer interface [polypeptide binding]; other site 1427342012855 acyl-activating enzyme (AAE) consensus motif; other site 1427342012856 putative active site [active] 1427342012857 putative AMP binding site [chemical binding]; other site 1427342012858 putative CoA binding site [chemical binding]; other site 1427342012859 chemical substrate binding site [chemical binding]; other site 1427342012860 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1427342012861 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 1427342012862 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1427342012863 DNA binding site [nucleotide binding] 1427342012864 active site 1427342012865 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 1427342012866 PapC N-terminal domain; Region: PapC_N; pfam13954 1427342012867 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 1427342012868 PapC C-terminal domain; Region: PapC_C; pfam13953 1427342012869 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 1427342012870 Hydrolase of X-linked nucleoside diphosphate N terminal; Region: Nudix_N; pfam12535 1427342012871 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_14; cd04672 1427342012872 nudix motif; other site 1427342012873 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1427342012874 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342012875 P-loop; other site 1427342012876 Magnesium ion binding site [ion binding]; other site 1427342012877 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342012878 Magnesium ion binding site [ion binding]; other site 1427342012879 Protein of unknown function (DUF2786); Region: DUF2786; pfam10979 1427342012880 HNH endonuclease; Region: HNH_3; pfam13392 1427342012881 replicative DNA helicase; Region: DnaB; TIGR00665 1427342012882 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1427342012883 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 1427342012884 Walker A motif; other site 1427342012885 ATP binding site [chemical binding]; other site 1427342012886 Walker B motif; other site 1427342012887 DNA binding loops [nucleotide binding] 1427342012888 Nucleoid-associated protein [General function prediction only]; Region: COG3081 1427342012889 nucleoid-associated protein NdpA; Validated; Region: PRK00378 1427342012890 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1427342012891 Arc-like DNA binding domain; Region: Arc; pfam03869 1427342012892 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 1427342012893 ParB-like nuclease domain; Region: ParB; smart00470 1427342012894 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 1427342012895 integrating conjugative element protein, PFL_4669 family; Region: ICE_PFL4669; TIGR03761 1427342012896 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 1427342012897 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1427342012898 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 1427342012899 dimer interface [polypeptide binding]; other site 1427342012900 ssDNA binding site [nucleotide binding]; other site 1427342012901 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1427342012902 DNA topoisomerase I, bacterial; Region: topA_bact; TIGR01051 1427342012903 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 1427342012904 active site 1427342012905 metal binding site [ion binding]; metal-binding site 1427342012906 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 1427342012907 domain I; other site 1427342012908 DNA binding groove [nucleotide binding] 1427342012909 phosphate binding site [ion binding]; other site 1427342012910 domain II; other site 1427342012911 domain III; other site 1427342012912 nucleotide binding site [chemical binding]; other site 1427342012913 catalytic site [active] 1427342012914 domain IV; other site 1427342012915 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342012916 DNA-binding site [nucleotide binding]; DNA binding site 1427342012917 RNA-binding motif; other site 1427342012918 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342012919 ATP binding site [chemical binding]; other site 1427342012920 putative Mg++ binding site [ion binding]; other site 1427342012921 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 1427342012922 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342012923 nucleotide binding region [chemical binding]; other site 1427342012924 ATP-binding site [chemical binding]; other site 1427342012925 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 1427342012926 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 1427342012927 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 1427342012928 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 1427342012929 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 1427342012930 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342012931 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 1427342012932 type IV pilus biogenesis protein PilP; Region: pilP_fam; TIGR03021 1427342012933 Type II/IV secretion system protein; Region: T2SE; pfam00437 1427342012934 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342012935 Walker A motif; other site 1427342012936 ATP binding site [chemical binding]; other site 1427342012937 Walker B motif; other site 1427342012938 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342012939 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342012940 PilS N terminal; Region: PilS; pfam08805 1427342012941 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 1427342012942 PilM; Region: PilM; pfam07419 1427342012943 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 1427342012944 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 1427342012945 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1427342012946 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 1427342012947 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1427342012948 Catalytic site [active] 1427342012949 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 1427342012950 integrating conjugative element protein, PFL_4695 family; Region: ICE_PFL_4695; TIGR03765 1427342012951 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 1427342012952 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 1427342012953 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 1427342012954 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1427342012955 Family description; Region: UvrD_C_2; pfam13538 1427342012956 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 1427342012957 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 1427342012958 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 1427342012959 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 1427342012960 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 1427342012961 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 1427342012962 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 1427342012963 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 1427342012964 Protein of unknown function (DUF972); Region: DUF972; pfam06156 1427342012965 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 1427342012966 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 1427342012967 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 1427342012968 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1427342012969 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342012970 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1427342012971 Thioredoxin; Region: Thioredoxin_4; cl17273 1427342012972 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342012973 classical (c) SDRs; Region: SDR_c; cd05233 1427342012974 NAD(P) binding site [chemical binding]; other site 1427342012975 active site 1427342012976 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1427342012977 multiple promoter invertase; Provisional; Region: mpi; PRK13413 1427342012978 catalytic residues [active] 1427342012979 catalytic nucleophile [active] 1427342012980 Presynaptic Site I dimer interface [polypeptide binding]; other site 1427342012981 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 1427342012982 Synaptic Flat tetramer interface [polypeptide binding]; other site 1427342012983 Synaptic Site I dimer interface [polypeptide binding]; other site 1427342012984 DNA binding site [nucleotide binding] 1427342012985 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 1427342012986 DNA-binding interface [nucleotide binding]; DNA binding site 1427342012987 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 1427342012988 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 1427342012989 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 1427342012990 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 1427342012991 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 1427342012992 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 1427342012993 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 1427342012994 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 1427342012995 Putative helicase; Region: TraI_2; pfam07514 1427342012996 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 1427342012997 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342012998 HTH-like domain; Region: HTH_21; pfam13276 1427342012999 Integrase core domain; Region: rve; pfam00665 1427342013000 Integrase core domain; Region: rve_3; pfam13683 1427342013001 Transposase; Region: HTH_Tnp_1; pfam01527 1427342013002 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 1427342013003 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 1427342013004 active site 1427342013005 catalytic residues [active] 1427342013006 DNA binding site [nucleotide binding] 1427342013007 Int/Topo IB signature motif; other site 1427342013008 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 1427342013009 Ligand Binding Site [chemical binding]; other site 1427342013010 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 1427342013011 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342013012 FeS/SAM binding site; other site 1427342013013 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 1427342013014 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342013015 binding surface 1427342013016 TPR motif; other site 1427342013017 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342013018 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342013019 ligand binding site [chemical binding]; other site 1427342013020 translocation protein TolB; Provisional; Region: tolB; PRK00178 1427342013021 TolB amino-terminal domain; Region: TolB_N; pfam04052 1427342013022 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1427342013023 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1427342013024 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1427342013025 TolA protein; Region: tolA_full; TIGR02794 1427342013026 TolA protein; Region: tolA_full; TIGR02794 1427342013027 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 1427342013028 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1427342013029 TolR protein; Region: tolR; TIGR02801 1427342013030 TolQ protein; Region: tolQ; TIGR02796 1427342013031 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342013032 active site 1427342013033 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1427342013034 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342013035 Walker A motif; other site 1427342013036 ATP binding site [chemical binding]; other site 1427342013037 Walker B motif; other site 1427342013038 arginine finger; other site 1427342013039 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1427342013040 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1427342013041 RuvA N terminal domain; Region: RuvA_N; pfam01330 1427342013042 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1427342013043 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 1427342013044 dimer interface [polypeptide binding]; other site 1427342013045 active site 1427342013046 putative DNA-binding cleft [nucleotide binding]; other site 1427342013047 hypothetical protein; Validated; Region: PRK00110 1427342013048 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1427342013049 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 1427342013050 dimer interface [polypeptide binding]; other site 1427342013051 anticodon binding site; other site 1427342013052 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 1427342013053 homodimer interface [polypeptide binding]; other site 1427342013054 motif 1; other site 1427342013055 active site 1427342013056 motif 2; other site 1427342013057 GAD domain; Region: GAD; pfam02938 1427342013058 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 1427342013059 active site 1427342013060 motif 3; other site 1427342013061 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1427342013062 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1427342013063 dimerization interface [polypeptide binding]; other site 1427342013064 DPS ferroxidase diiron center [ion binding]; other site 1427342013065 ion pore; other site 1427342013066 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1427342013067 DNA-binding site [nucleotide binding]; DNA binding site 1427342013068 RNA-binding motif; other site 1427342013069 hypothetical protein; Provisional; Region: PRK00295 1427342013070 HIT domain; Region: HIT; pfam01230 1427342013071 nucleotide binding site/active site [active] 1427342013072 HIT family signature motif; other site 1427342013073 catalytic residue [active] 1427342013074 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342013075 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342013076 CoenzymeA binding site [chemical binding]; other site 1427342013077 subunit interaction site [polypeptide binding]; other site 1427342013078 PHB binding site; other site 1427342013079 prolyl-tRNA synthetase; Provisional; Region: PRK09194 1427342013080 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 1427342013081 dimer interface [polypeptide binding]; other site 1427342013082 motif 1; other site 1427342013083 active site 1427342013084 motif 2; other site 1427342013085 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 1427342013086 putative deacylase active site [active] 1427342013087 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 1427342013088 active site 1427342013089 motif 3; other site 1427342013090 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 1427342013091 anticodon binding site; other site 1427342013092 acylphosphatase; Provisional; Region: PRK14442 1427342013093 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 1427342013094 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342013095 catalytic residues [active] 1427342013096 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 1427342013097 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 1427342013098 ArsC family; Region: ArsC; pfam03960 1427342013099 catalytic residues [active] 1427342013100 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1427342013101 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342013102 Predicted membrane protein [Function unknown]; Region: COG3308 1427342013103 DNA replication initiation factor; Validated; Region: PRK05642 1427342013104 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1427342013105 Walker A motif; other site 1427342013106 ATP binding site [chemical binding]; other site 1427342013107 Walker B motif; other site 1427342013108 arginine finger; other site 1427342013109 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 1427342013110 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 1427342013111 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 1427342013112 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 1427342013113 dimerization interface [polypeptide binding]; other site 1427342013114 putative ATP binding site [chemical binding]; other site 1427342013115 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 1427342013116 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 1427342013117 active site 1427342013118 substrate binding site [chemical binding]; other site 1427342013119 cosubstrate binding site; other site 1427342013120 catalytic site [active] 1427342013121 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 1427342013122 Transcriptional regulators [Transcription]; Region: MarR; COG1846 1427342013123 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342013124 putative DNA binding site [nucleotide binding]; other site 1427342013125 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 1427342013126 Domain of unknown function (DUF2024); Region: DUF2024; pfam09630 1427342013127 Transcriptional antiterminator [Transcription]; Region: Rof; COG4568 1427342013128 Chain length determinant protein [Cell envelope biogenesis, outer membrane]; Region: WzzB; COG3765 1427342013129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3122 1427342013130 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 1427342013131 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 1427342013132 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 1427342013133 homodimer interface [polypeptide binding]; other site 1427342013134 metal binding site [ion binding]; metal-binding site 1427342013135 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 1427342013136 homodimer interface [polypeptide binding]; other site 1427342013137 active site 1427342013138 putative chemical substrate binding site [chemical binding]; other site 1427342013139 metal binding site [ion binding]; metal-binding site 1427342013140 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1427342013141 HD domain; Region: HD_4; pfam13328 1427342013142 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1427342013143 synthetase active site [active] 1427342013144 NTP binding site [chemical binding]; other site 1427342013145 metal binding site [ion binding]; metal-binding site 1427342013146 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 1427342013147 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 1427342013148 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 1427342013149 TRAM domain; Region: TRAM; pfam01938 1427342013150 cysteine synthase B; Region: cysM; TIGR01138 1427342013151 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 1427342013152 dimer interface [polypeptide binding]; other site 1427342013153 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342013154 catalytic residue [active] 1427342013155 outer membrane receptor FepA; Provisional; Region: PRK13528 1427342013156 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342013157 N-terminal plug; other site 1427342013158 ligand-binding site [chemical binding]; other site 1427342013159 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342013160 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342013161 dimerization interface [polypeptide binding]; other site 1427342013162 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342013163 dimer interface [polypeptide binding]; other site 1427342013164 phosphorylation site [posttranslational modification] 1427342013165 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342013166 ATP binding site [chemical binding]; other site 1427342013167 G-X-G motif; other site 1427342013168 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342013169 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342013170 active site 1427342013171 phosphorylation site [posttranslational modification] 1427342013172 intermolecular recognition site; other site 1427342013173 dimerization interface [polypeptide binding]; other site 1427342013174 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342013175 DNA binding site [nucleotide binding] 1427342013176 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342013177 ATP binding site [chemical binding]; other site 1427342013178 Mg2+ binding site [ion binding]; other site 1427342013179 G-X-G motif; other site 1427342013180 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342013181 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342013182 active site 1427342013183 phosphorylation site [posttranslational modification] 1427342013184 intermolecular recognition site; other site 1427342013185 dimerization interface [polypeptide binding]; other site 1427342013186 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 1427342013187 putative binding surface; other site 1427342013188 active site 1427342013189 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 1427342013190 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 1427342013191 putative ligand binding site [chemical binding]; other site 1427342013192 putative NAD binding site [chemical binding]; other site 1427342013193 catalytic site [active] 1427342013194 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 1427342013195 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 1427342013196 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 1427342013197 Sulfatase; Region: Sulfatase; cl17466 1427342013198 DNA polymerase IV; Validated; Region: PRK02406 1427342013199 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 1427342013200 DNA binding site [nucleotide binding] 1427342013201 active site 1427342013202 Replication protein A C terminal; Region: RPA_C; pfam08784 1427342013203 Predicted integral membrane protein [Function unknown]; Region: COG0392 1427342013204 Uncharacterized conserved protein [Function unknown]; Region: COG2898 1427342013205 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 1427342013206 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 1427342013207 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 1427342013208 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1427342013209 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 1427342013210 potassium uptake protein; Region: kup; TIGR00794 1427342013211 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 1427342013212 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1427342013213 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 1427342013214 FeS/SAM binding site; other site 1427342013215 TRAM domain; Region: TRAM; pfam01938 1427342013216 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 1427342013217 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 1427342013218 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 1427342013219 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1427342013220 MgtE intracellular N domain; Region: MgtE_N; smart00924 1427342013221 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 1427342013222 Divalent cation transporter; Region: MgtE; pfam01769 1427342013223 Protein of unknown function (DUF754); Region: DUF754; pfam05449 1427342013224 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342013225 non-specific DNA binding site [nucleotide binding]; other site 1427342013226 Predicted transcriptional regulator [Transcription]; Region: COG2932 1427342013227 salt bridge; other site 1427342013228 sequence-specific DNA binding site [nucleotide binding]; other site 1427342013229 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1427342013230 Catalytic site [active] 1427342013231 Global regulator protein family; Region: CsrA; cl00670 1427342013232 aspartate kinase; Reviewed; Region: PRK06635 1427342013233 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 1427342013234 putative nucleotide binding site [chemical binding]; other site 1427342013235 putative catalytic residues [active] 1427342013236 putative Mg ion binding site [ion binding]; other site 1427342013237 putative aspartate binding site [chemical binding]; other site 1427342013238 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 1427342013239 putative allosteric regulatory site; other site 1427342013240 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 1427342013241 putative allosteric regulatory residue; other site 1427342013242 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1427342013243 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 1427342013244 motif 1; other site 1427342013245 active site 1427342013246 motif 2; other site 1427342013247 motif 3; other site 1427342013248 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1427342013249 DHHA1 domain; Region: DHHA1; pfam02272 1427342013250 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 1427342013251 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 1427342013252 tetramer interface [polypeptide binding]; other site 1427342013253 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342013254 catalytic residue [active] 1427342013255 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 1427342013256 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 1427342013257 putative active site [active] 1427342013258 Zn binding site [ion binding]; other site 1427342013259 succinylarginine dihydrolase; Provisional; Region: PRK13281 1427342013260 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 1427342013261 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 1427342013262 NAD(P) binding site [chemical binding]; other site 1427342013263 catalytic residues [active] 1427342013264 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 1427342013265 arginine N-succinyltransferase; Region: arg_catab_AstA; TIGR03244 1427342013266 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 1427342013267 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 1427342013268 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 1427342013269 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342013270 inhibitor-cofactor binding pocket; inhibition site 1427342013271 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342013272 catalytic residue [active] 1427342013273 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 1427342013274 conserved cys residue [active] 1427342013275 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013276 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342013277 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013278 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 1427342013279 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342013280 Walker A/P-loop; other site 1427342013281 ATP binding site [chemical binding]; other site 1427342013282 Q-loop/lid; other site 1427342013283 ABC transporter signature motif; other site 1427342013284 Walker B; other site 1427342013285 D-loop; other site 1427342013286 H-loop/switch region; other site 1427342013287 Predicted deacylase [General function prediction only]; Region: COG3608 1427342013288 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 1427342013289 active site 1427342013290 Zn binding site [ion binding]; other site 1427342013291 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342013292 dimer interface [polypeptide binding]; other site 1427342013293 conserved gate region; other site 1427342013294 putative PBP binding loops; other site 1427342013295 ABC-ATPase subunit interface; other site 1427342013296 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342013297 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342013298 dimer interface [polypeptide binding]; other site 1427342013299 conserved gate region; other site 1427342013300 putative PBP binding loops; other site 1427342013301 ABC-ATPase subunit interface; other site 1427342013302 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 1427342013303 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342013304 substrate binding pocket [chemical binding]; other site 1427342013305 membrane-bound complex binding site; other site 1427342013306 hinge residues; other site 1427342013307 acetyl-CoA synthetase; Provisional; Region: PRK00174 1427342013308 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 1427342013309 active site 1427342013310 CoA binding site [chemical binding]; other site 1427342013311 acyl-activating enzyme (AAE) consensus motif; other site 1427342013312 AMP binding site [chemical binding]; other site 1427342013313 acetate binding site [chemical binding]; other site 1427342013314 DctM-like transporters; Region: DctM; pfam06808 1427342013315 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 1427342013316 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 1427342013317 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 1427342013318 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 1427342013319 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 1427342013320 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1427342013321 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1427342013322 MmgE/PrpD family; Region: MmgE_PrpD; pfam03972 1427342013323 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 1427342013324 dimer interface [polypeptide binding]; other site 1427342013325 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342013326 metal binding site [ion binding]; metal-binding site 1427342013327 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342013328 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342013329 active site 1427342013330 Uncharacterized conserved protein [Function unknown]; Region: COG3777 1427342013331 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342013332 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342013333 active site 2 [active] 1427342013334 active site 1 [active] 1427342013335 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013336 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013337 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 1427342013338 putative dimerization interface [polypeptide binding]; other site 1427342013339 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013340 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013341 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 1427342013342 putative effector binding pocket; other site 1427342013343 dimerization interface [polypeptide binding]; other site 1427342013344 Fusaric acid resistance protein family; Region: FUSC; pfam04632 1427342013345 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1427342013346 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 1427342013347 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 1427342013348 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 1427342013349 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 1427342013350 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342013351 putative active site [active] 1427342013352 heme pocket [chemical binding]; other site 1427342013353 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342013354 Walker A motif; other site 1427342013355 ATP binding site [chemical binding]; other site 1427342013356 Walker B motif; other site 1427342013357 arginine finger; other site 1427342013358 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 1427342013359 cofactor binding site; other site 1427342013360 metal binding site [ion binding]; metal-binding site 1427342013361 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 1427342013362 aromatic arch; other site 1427342013363 DCoH dimer interaction site [polypeptide binding]; other site 1427342013364 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1427342013365 DCoH tetramer interaction site [polypeptide binding]; other site 1427342013366 substrate binding site [chemical binding]; other site 1427342013367 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 1427342013368 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342013369 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342013370 homodimer interface [polypeptide binding]; other site 1427342013371 catalytic residue [active] 1427342013372 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 1427342013373 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1427342013374 hypothetical protein; Provisional; Region: PRK09256 1427342013375 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1427342013376 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 1427342013377 Predicted periplasmic protein [General function prediction only]; Region: COG3895 1427342013378 aromatic amino acid transporter; Provisional; Region: PRK10238 1427342013379 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 1427342013380 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 1427342013381 dimer interface [polypeptide binding]; other site 1427342013382 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 1427342013383 active site 1427342013384 Fe binding site [ion binding]; other site 1427342013385 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342013386 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013387 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013388 Protein of unknown function (DUF1427); Region: DUF1427; pfam07235 1427342013389 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 1427342013390 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 1427342013391 putative NAD(P) binding site [chemical binding]; other site 1427342013392 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism]; Region: COG5424 1427342013393 PAS domain S-box; Region: sensory_box; TIGR00229 1427342013394 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342013395 putative active site [active] 1427342013396 heme pocket [chemical binding]; other site 1427342013397 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342013398 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342013399 metal binding site [ion binding]; metal-binding site 1427342013400 active site 1427342013401 I-site; other site 1427342013402 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342013403 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342013404 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342013405 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342013406 Walker A/P-loop; other site 1427342013407 ATP binding site [chemical binding]; other site 1427342013408 Q-loop/lid; other site 1427342013409 ABC transporter signature motif; other site 1427342013410 Walker B; other site 1427342013411 D-loop; other site 1427342013412 H-loop/switch region; other site 1427342013413 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 1427342013414 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 1427342013415 catalytic residues [active] 1427342013416 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 1427342013417 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1427342013418 active site residue [active] 1427342013419 BolA-like protein; Region: BolA; cl00386 1427342013420 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 1427342013421 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 1427342013422 fumarate hydratase; Provisional; Region: PRK12425 1427342013423 Class II fumarases; Region: Fumarase_classII; cd01362 1427342013424 active site 1427342013425 tetramer interface [polypeptide binding]; other site 1427342013426 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1427342013427 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342013428 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3397 1427342013429 Chitin binding domain; Region: Chitin_bind_3; pfam03067 1427342013430 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1427342013431 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1427342013432 tetramer interface [polypeptide binding]; other site 1427342013433 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342013434 catalytic residue [active] 1427342013435 MAPEG family; Region: MAPEG; pfam01124 1427342013436 thioredoxin reductase; Provisional; Region: PRK10262 1427342013437 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342013438 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342013439 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1427342013440 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 1427342013441 dimer interface [polypeptide binding]; other site 1427342013442 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1427342013443 catalytic triad [active] 1427342013444 peroxidatic and resolving cysteines [active] 1427342013445 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3322 1427342013446 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342013447 dimerization interface [polypeptide binding]; other site 1427342013448 PAS domain S-box; Region: sensory_box; TIGR00229 1427342013449 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342013450 putative active site [active] 1427342013451 heme pocket [chemical binding]; other site 1427342013452 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342013453 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342013454 metal binding site [ion binding]; metal-binding site 1427342013455 active site 1427342013456 I-site; other site 1427342013457 putative sulfate transport protein CysZ; Validated; Region: PRK04949 1427342013458 Neutral/alkaline non-lysosomal ceramidase; Region: Ceramidase_alk; pfam04734 1427342013459 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 1427342013460 Phosphoesterase family; Region: Phosphoesterase; pfam04185 1427342013461 Domain of unknown function (DUF756); Region: DUF756; pfam05506 1427342013462 Domain of unknown function (DUF756); Region: DUF756; pfam05506 1427342013463 phospholipase C accessory protein PlcR; Region: plc_access_R; TIGR03398 1427342013464 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342013465 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 1427342013466 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DegV; COG1307 1427342013467 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 1427342013468 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342013469 Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_5_FMN; cd04747 1427342013470 putative active site [active] 1427342013471 putative FMN binding site [chemical binding]; other site 1427342013472 putative substrate binding site [chemical binding]; other site 1427342013473 putative catalytic residue [active] 1427342013474 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342013475 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342013476 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 1427342013477 catalytic residues [active] 1427342013478 dimer interface [polypeptide binding]; other site 1427342013479 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 1427342013480 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342013481 Protein of unknown function (DUF3565); Region: DUF3565; pfam12088 1427342013482 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 1427342013483 propionate/acetate kinase; Provisional; Region: PRK12379 1427342013484 phosphate acetyltransferase; Reviewed; Region: PRK05632 1427342013485 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 1427342013486 DRTGG domain; Region: DRTGG; pfam07085 1427342013487 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 1427342013488 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342013489 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 1427342013490 putative acyl-acceptor binding pocket; other site 1427342013491 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342013492 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342013493 ligand binding site [chemical binding]; other site 1427342013494 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1427342013495 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342013496 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342013497 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013498 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 1427342013499 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 1427342013500 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342013501 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1427342013502 mycofactocin system transcriptional regulator; Region: mycofact_TetR; TIGR03968 1427342013503 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342013504 HTH-like domain; Region: HTH_21; pfam13276 1427342013505 Integrase core domain; Region: rve; pfam00665 1427342013506 DDE domain; Region: DDE_Tnp_IS240; pfam13610 1427342013507 Integrase core domain; Region: rve_3; pfam13683 1427342013508 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 1427342013509 Transposase; Region: HTH_Tnp_1; pfam01527 1427342013510 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 1427342013511 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342013512 putative metal binding site [ion binding]; other site 1427342013513 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013514 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013515 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 1427342013516 putative dimerization interface [polypeptide binding]; other site 1427342013517 cell density-dependent motility repressor; Provisional; Region: PRK10082 1427342013518 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013519 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342013520 dimerization interface [polypeptide binding]; other site 1427342013521 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 1427342013522 homotrimer interaction site [polypeptide binding]; other site 1427342013523 putative active site [active] 1427342013524 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1427342013525 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342013526 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342013527 catalytic residue [active] 1427342013528 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 1427342013529 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342013530 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342013531 putative substrate translocation pore; other site 1427342013532 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 1427342013533 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342013534 motif II; other site 1427342013535 manganese transport protein MntH; Reviewed; Region: PRK00701 1427342013536 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 1427342013537 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_8; cd08901 1427342013538 putative hydrophobic ligand binding site [chemical binding]; other site 1427342013539 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1427342013540 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1427342013541 amidase catalytic site [active] 1427342013542 Zn binding residues [ion binding]; other site 1427342013543 substrate binding site [chemical binding]; other site 1427342013544 Predicted membrane protein [Function unknown]; Region: COG4270 1427342013545 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342013546 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342013547 active site 1427342013548 catalytic tetrad [active] 1427342013549 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_14; cd08355 1427342013550 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342013551 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 1427342013552 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342013553 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 1427342013554 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342013555 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 1427342013556 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342013557 ATP binding site [chemical binding]; other site 1427342013558 putative Mg++ binding site [ion binding]; other site 1427342013559 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342013560 nucleotide binding region [chemical binding]; other site 1427342013561 ATP-binding site [chemical binding]; other site 1427342013562 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342013563 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342013564 S-adenosylmethionine binding site [chemical binding]; other site 1427342013565 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342013566 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342013567 DNA-binding site [nucleotide binding]; DNA binding site 1427342013568 FCD domain; Region: FCD; pfam07729 1427342013569 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 1427342013570 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 1427342013571 tetramer interface [polypeptide binding]; other site 1427342013572 active site 1427342013573 Mg2+/Mn2+ binding site [ion binding]; other site 1427342013574 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1427342013575 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 1427342013576 dimer interface [polypeptide binding]; other site 1427342013577 active site 1427342013578 citrylCoA binding site [chemical binding]; other site 1427342013579 oxalacetate/citrate binding site [chemical binding]; other site 1427342013580 coenzyme A binding site [chemical binding]; other site 1427342013581 catalytic triad [active] 1427342013582 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 1427342013583 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1427342013584 substrate binding site [chemical binding]; other site 1427342013585 ligand binding site [chemical binding]; other site 1427342013586 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 1427342013587 substrate binding site [chemical binding]; other site 1427342013588 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 1427342013589 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 1427342013590 2-methylcitrate dehydratase; Region: prpD; TIGR02330 1427342013591 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342013592 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342013593 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013594 Predicted permeases [General function prediction only]; Region: COG0730 1427342013595 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 1427342013596 Spore germination protein; Region: Spore_permease; cl17796 1427342013597 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 1427342013598 Transglycosylase; Region: Transgly; cl17702 1427342013599 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1427342013600 Predicted ATPase [General function prediction only]; Region: COG4637 1427342013601 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342013602 Walker A/P-loop; other site 1427342013603 ATP binding site [chemical binding]; other site 1427342013604 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 1427342013605 Acyl carrier protein phosphodiesterase [Lipid metabolism]; Region: AcpD; COG1182 1427342013606 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342013607 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342013608 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013609 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342013610 dimerization interface [polypeptide binding]; other site 1427342013611 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1427342013612 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 1427342013613 Na binding site [ion binding]; other site 1427342013614 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 1427342013615 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 1427342013616 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 1427342013617 Glutamate binding site [chemical binding]; other site 1427342013618 NAD binding site [chemical binding]; other site 1427342013619 catalytic residues [active] 1427342013620 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 1427342013621 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342013622 N-terminal plug; other site 1427342013623 ligand-binding site [chemical binding]; other site 1427342013624 Cupin domain; Region: Cupin_2; cl17218 1427342013625 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342013626 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013627 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013628 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1427342013629 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342013630 Walker A motif; other site 1427342013631 ATP binding site [chemical binding]; other site 1427342013632 Walker B motif; other site 1427342013633 arginine finger; other site 1427342013634 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1427342013635 Predicted secreted protein [Function unknown]; Region: COG5513 1427342013636 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342013637 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 1427342013638 membrane-bound complex binding site; other site 1427342013639 hinge residues; other site 1427342013640 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342013641 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342013642 S-adenosylmethionine binding site [chemical binding]; other site 1427342013643 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342013644 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342013645 S-adenosylmethionine binding site [chemical binding]; other site 1427342013646 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 1427342013647 active site 1427342013648 hydrophilic channel; other site 1427342013649 dimerization interface [polypeptide binding]; other site 1427342013650 catalytic residues [active] 1427342013651 active site lid [active] 1427342013652 Recombination protein O N terminal; Region: RecO_N; pfam11967 1427342013653 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1427342013654 Recombination protein O C terminal; Region: RecO_C; pfam02565 1427342013655 GTPase Era; Reviewed; Region: era; PRK00089 1427342013656 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1427342013657 G1 box; other site 1427342013658 GTP/Mg2+ binding site [chemical binding]; other site 1427342013659 Switch I region; other site 1427342013660 G2 box; other site 1427342013661 Switch II region; other site 1427342013662 G3 box; other site 1427342013663 G4 box; other site 1427342013664 G5 box; other site 1427342013665 KH domain; Region: KH_2; pfam07650 1427342013666 ribonuclease III; Reviewed; Region: rnc; PRK00102 1427342013667 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 1427342013668 dimerization interface [polypeptide binding]; other site 1427342013669 active site 1427342013670 metal binding site [ion binding]; metal-binding site 1427342013671 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 1427342013672 dsRNA binding site [nucleotide binding]; other site 1427342013673 signal peptidase I; Provisional; Region: PRK10861 1427342013674 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 1427342013675 Catalytic site [active] 1427342013676 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 1427342013677 GTP-binding protein LepA; Provisional; Region: PRK05433 1427342013678 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1427342013679 G1 box; other site 1427342013680 putative GEF interaction site [polypeptide binding]; other site 1427342013681 GTP/Mg2+ binding site [chemical binding]; other site 1427342013682 Switch I region; other site 1427342013683 G2 box; other site 1427342013684 G3 box; other site 1427342013685 Switch II region; other site 1427342013686 G4 box; other site 1427342013687 G5 box; other site 1427342013688 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 1427342013689 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 1427342013690 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1427342013691 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1427342013692 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1427342013693 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 1427342013694 protein binding site [polypeptide binding]; other site 1427342013695 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 1427342013696 protein binding site [polypeptide binding]; other site 1427342013697 Positive regulator of sigma E activity [Signal transduction mechanisms]; Region: RseC; COG3086 1427342013698 MucB/RseB family; Region: MucB_RseB; pfam03888 1427342013699 anti-sigma E factor; Provisional; Region: rseB; PRK09455 1427342013700 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 1427342013701 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342013702 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342013703 DNA binding residues [nucleotide binding] 1427342013704 L-aspartate oxidase; Provisional; Region: PRK09077 1427342013705 L-aspartate oxidase; Provisional; Region: PRK06175 1427342013706 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1427342013707 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1427342013708 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1427342013709 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1427342013710 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 1427342013711 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 1427342013712 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342013713 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342013714 dimer interface [polypeptide binding]; other site 1427342013715 phosphorylation site [posttranslational modification] 1427342013716 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342013717 ATP binding site [chemical binding]; other site 1427342013718 G-X-G motif; other site 1427342013719 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 1427342013720 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342013721 active site 1427342013722 phosphorylation site [posttranslational modification] 1427342013723 intermolecular recognition site; other site 1427342013724 dimerization interface [polypeptide binding]; other site 1427342013725 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342013726 DNA binding site [nucleotide binding] 1427342013727 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342013728 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 1427342013729 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 1427342013730 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 1427342013731 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 1427342013732 Putative ammonia monooxygenase; Region: AmoA; pfam05145 1427342013733 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 1427342013734 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 1427342013735 ligand binding site [chemical binding]; other site 1427342013736 active site 1427342013737 UGI interface [polypeptide binding]; other site 1427342013738 catalytic site [active] 1427342013739 Uncharacterized vancomycin resistance protein [Defense mechanisms]; Region: COG2720 1427342013740 VanW like protein; Region: VanW; pfam04294 1427342013741 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342013742 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342013743 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013744 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013745 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 1427342013746 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 1427342013747 tetrameric interface [polypeptide binding]; other site 1427342013748 NAD binding site [chemical binding]; other site 1427342013749 catalytic residues [active] 1427342013750 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342013751 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 1427342013752 substrate binding pocket [chemical binding]; other site 1427342013753 FAD binding site [chemical binding]; other site 1427342013754 catalytic base [active] 1427342013755 enoyl-CoA hydratase; Provisional; Region: PRK09076 1427342013756 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342013757 substrate binding site [chemical binding]; other site 1427342013758 oxyanion hole (OAH) forming residues; other site 1427342013759 trimer interface [polypeptide binding]; other site 1427342013760 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 1427342013761 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342013762 substrate binding site [chemical binding]; other site 1427342013763 oxyanion hole (OAH) forming residues; other site 1427342013764 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 1427342013765 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1427342013766 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 1427342013767 Ion channel; Region: Ion_trans_2; pfam07885 1427342013768 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 1427342013769 NADH(P)-binding; Region: NAD_binding_10; pfam13460 1427342013770 NAD binding site [chemical binding]; other site 1427342013771 substrate binding site [chemical binding]; other site 1427342013772 putative active site [active] 1427342013773 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 1427342013774 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342013775 SCP-2 sterol transfer family; Region: SCP2; pfam02036 1427342013776 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013777 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013778 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342013779 dimerization interface [polypeptide binding]; other site 1427342013780 Predicted membrane protein [Function unknown]; Region: COG3776 1427342013781 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 1427342013782 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1427342013783 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342013784 RNA binding surface [nucleotide binding]; other site 1427342013785 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 1427342013786 active site 1427342013787 uracil binding [chemical binding]; other site 1427342013788 hypothetical protein; Provisional; Region: PRK06132 1427342013789 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1427342013790 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 1427342013791 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342013792 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 1427342013793 hypothetical protein; Provisional; Region: PRK13687 1427342013794 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342013795 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342013796 Coenzyme A binding pocket [chemical binding]; other site 1427342013797 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342013798 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 1427342013799 dimer interface [polypeptide binding]; other site 1427342013800 active site 1427342013801 metal binding site [ion binding]; metal-binding site 1427342013802 glutathione binding site [chemical binding]; other site 1427342013803 Uncharacterized conserved protein [Function unknown]; Region: COG1359 1427342013804 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013805 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013806 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342013807 dimerization interface [polypeptide binding]; other site 1427342013808 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 1427342013809 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 1427342013810 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1427342013811 trimer interface [polypeptide binding]; other site 1427342013812 active site 1427342013813 substrate binding site [chemical binding]; other site 1427342013814 CoA binding site [chemical binding]; other site 1427342013815 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342013816 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 1427342013817 active site 1427342013818 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1427342013819 trimer interface [polypeptide binding]; other site 1427342013820 active site 1427342013821 substrate binding site [chemical binding]; other site 1427342013822 CoA binding site [chemical binding]; other site 1427342013823 amidase; Provisional; Region: PRK07042 1427342013824 Amidase; Region: Amidase; pfam01425 1427342013825 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342013826 metabolite-proton symporter; Region: 2A0106; TIGR00883 1427342013827 putative substrate translocation pore; other site 1427342013828 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 1427342013829 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 1427342013830 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342013831 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342013832 LysR substrate binding domain; Region: LysR_substrate; pfam03466 1427342013833 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK02998 1427342013834 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1427342013835 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 1427342013836 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 1427342013837 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1427342013838 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1427342013839 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1427342013840 Uncharacterized conserved protein [Function unknown]; Region: COG5306 1427342013841 Domain of unknown function (DUF2341); Region: DUF2341; pfam10102 1427342013842 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 1427342013843 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1427342013844 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 1427342013845 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 1427342013846 Surface antigen; Region: Bac_surface_Ag; pfam01103 1427342013847 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 1427342013848 haemagglutination activity domain; Region: Haemagg_act; pfam05860 1427342013849 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 1427342013850 ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PstS; COG0226 1427342013851 ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PstS; COG0226 1427342013852 type II secretion system protein F; Region: GspF; TIGR02120 1427342013853 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342013854 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342013855 type II secretion system protein E; Region: type_II_gspE; TIGR02533 1427342013856 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 1427342013857 Walker A motif; other site 1427342013858 ATP binding site [chemical binding]; other site 1427342013859 Walker B motif; other site 1427342013860 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342013861 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342013862 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342013863 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 1427342013864 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342013865 Type II secretory pathway, component PulM [Intracellular trafficking and secretion]; Region: PulM; COG3149 1427342013866 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 1427342013867 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 1427342013868 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1427342013869 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 1427342013870 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 1427342013871 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 1427342013872 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 1427342013873 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1427342013874 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 1427342013875 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 1427342013876 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1427342013877 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 1427342013878 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342013879 FecR protein; Region: FecR; pfam04773 1427342013880 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1427342013881 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342013882 DNA binding residues [nucleotide binding] 1427342013883 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342013884 TonB C terminal; Region: TonB_2; pfam13103 1427342013885 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 1427342013886 heme binding pocket [chemical binding]; other site 1427342013887 heme ligand [chemical binding]; other site 1427342013888 Cell division inhibitor SulA; Region: SulA; cl01880 1427342013889 DNA Polymerase Y-family; Region: PolY_like; cd03468 1427342013890 active site 1427342013891 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 1427342013892 DNA binding site [nucleotide binding] 1427342013893 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 1427342013894 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 1427342013895 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 1427342013896 putative active site [active] 1427342013897 putative PHP Thumb interface [polypeptide binding]; other site 1427342013898 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 1427342013899 generic binding surface II; other site 1427342013900 generic binding surface I; other site 1427342013901 exonuclease subunit SbcD; Provisional; Region: PRK10966 1427342013902 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 1427342013903 active site 1427342013904 metal binding site [ion binding]; metal-binding site 1427342013905 DNA binding site [nucleotide binding] 1427342013906 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 1427342013907 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342013908 AAA domain; Region: AAA_23; pfam13476 1427342013909 Walker A/P-loop; other site 1427342013910 ATP binding site [chemical binding]; other site 1427342013911 Q-loop/lid; other site 1427342013912 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342013913 ABC transporter signature motif; other site 1427342013914 Walker B; other site 1427342013915 D-loop; other site 1427342013916 H-loop/switch region; other site 1427342013917 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 1427342013918 AAA domain; Region: AAA_30; pfam13604 1427342013919 Family description; Region: UvrD_C_2; pfam13538 1427342013920 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 1427342013921 Family description; Region: UvrD_C_2; pfam13538 1427342013922 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 1427342013923 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 1427342013924 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 1427342013925 EamA-like transporter family; Region: EamA; pfam00892 1427342013926 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342013927 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342013928 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342013929 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 1427342013930 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 1427342013931 Chromate transporter; Region: Chromate_transp; pfam02417 1427342013932 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342013933 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342013934 dimer interface [polypeptide binding]; other site 1427342013935 putative CheW interface [polypeptide binding]; other site 1427342013936 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342013937 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342013938 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342013939 PAS fold; Region: PAS_3; pfam08447 1427342013940 putative active site [active] 1427342013941 heme pocket [chemical binding]; other site 1427342013942 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342013943 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342013944 putative active site [active] 1427342013945 heme pocket [chemical binding]; other site 1427342013946 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342013947 dimer interface [polypeptide binding]; other site 1427342013948 phosphorylation site [posttranslational modification] 1427342013949 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342013950 ATP binding site [chemical binding]; other site 1427342013951 Mg2+ binding site [ion binding]; other site 1427342013952 G-X-G motif; other site 1427342013953 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 1427342013954 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 1427342013955 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342013956 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342013957 active site 1427342013958 phosphorylation site [posttranslational modification] 1427342013959 intermolecular recognition site; other site 1427342013960 dimerization interface [polypeptide binding]; other site 1427342013961 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342013962 DNA binding residues [nucleotide binding] 1427342013963 dimerization interface [polypeptide binding]; other site 1427342013964 Predicted membrane protein [Function unknown]; Region: COG4655 1427342013965 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 1427342013966 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 1427342013967 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 1427342013968 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342013969 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 1427342013970 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342013971 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 1427342013972 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1427342013973 ATP binding site [chemical binding]; other site 1427342013974 Walker A motif; other site 1427342013975 hexamer interface [polypeptide binding]; other site 1427342013976 Walker B motif; other site 1427342013977 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 1427342013978 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 1427342013979 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 1427342013980 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 1427342013981 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342013982 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 1427342013983 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 1427342013984 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 1427342013985 Cache domain; Region: Cache_1; pfam02743 1427342013986 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342013987 dimerization interface [polypeptide binding]; other site 1427342013988 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342013989 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342013990 dimer interface [polypeptide binding]; other site 1427342013991 putative CheW interface [polypeptide binding]; other site 1427342013992 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 1427342013993 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 1427342013994 Cache domain; Region: Cache_1; pfam02743 1427342013995 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342013996 dimerization interface [polypeptide binding]; other site 1427342013997 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342013998 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342013999 dimer interface [polypeptide binding]; other site 1427342014000 putative CheW interface [polypeptide binding]; other site 1427342014001 Vibrio chemotaxis protein N terminus; Region: MCP_N; pfam05581 1427342014002 Cache domain; Region: Cache_1; pfam02743 1427342014003 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342014004 dimerization interface [polypeptide binding]; other site 1427342014005 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342014006 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342014007 dimer interface [polypeptide binding]; other site 1427342014008 putative CheW interface [polypeptide binding]; other site 1427342014009 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342014010 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 1427342014011 Predicted deacetylase [General function prediction only]; Region: COG3233 1427342014012 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u10; cd11374 1427342014013 putative active site [active] 1427342014014 putative Zn binding site [ion binding]; other site 1427342014015 Predicted integral membrane protein [Function unknown]; Region: COG0392 1427342014016 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 1427342014017 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 1427342014018 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 1427342014019 putative active site [active] 1427342014020 putative substrate binding site [chemical binding]; other site 1427342014021 putative cosubstrate binding site; other site 1427342014022 catalytic site [active] 1427342014023 exonuclease I; Provisional; Region: sbcB; PRK11779 1427342014024 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 1427342014025 active site 1427342014026 catalytic site [active] 1427342014027 substrate binding site [chemical binding]; other site 1427342014028 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 1427342014029 Protein of unknown function (DUF975); Region: DUF975; cl10504 1427342014030 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1427342014031 Uncharacterized membrane protein [Function unknown]; Region: SpoIIM; COG1300 1427342014032 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 1427342014033 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342014034 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1427342014035 Walker A motif; other site 1427342014036 ATP binding site [chemical binding]; other site 1427342014037 Walker B motif; other site 1427342014038 arginine finger; other site 1427342014039 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 1427342014040 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 1427342014041 metal ion-dependent adhesion site (MIDAS); other site 1427342014042 PilZ domain; Region: PilZ; pfam07238 1427342014043 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 1427342014044 universal stress protein UspE; Provisional; Region: PRK11175 1427342014045 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342014046 Ligand Binding Site [chemical binding]; other site 1427342014047 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342014048 Ligand Binding Site [chemical binding]; other site 1427342014049 pyruvate kinase; Provisional; Region: PRK05826 1427342014050 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 1427342014051 domain interfaces; other site 1427342014052 active site 1427342014053 enoyl-CoA hydratase; Provisional; Region: PRK06688 1427342014054 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342014055 substrate binding site [chemical binding]; other site 1427342014056 oxyanion hole (OAH) forming residues; other site 1427342014057 trimer interface [polypeptide binding]; other site 1427342014058 hypothetical protein; Provisional; Region: PRK05713 1427342014059 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342014060 catalytic loop [active] 1427342014061 iron binding site [ion binding]; other site 1427342014062 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 1427342014063 FAD binding pocket [chemical binding]; other site 1427342014064 conserved FAD binding motif [chemical binding]; other site 1427342014065 phosphate binding motif [ion binding]; other site 1427342014066 beta-alpha-beta structure motif; other site 1427342014067 NAD binding pocket [chemical binding]; other site 1427342014068 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342014069 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342014070 metal binding site [ion binding]; metal-binding site 1427342014071 active site 1427342014072 I-site; other site 1427342014073 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 1427342014074 Fumarase C-terminus; Region: Fumerase_C; pfam05683 1427342014075 manganese transport protein MntH; Reviewed; Region: PRK00701 1427342014076 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 1427342014077 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 1427342014078 intracellular protease, PfpI family; Region: PfpI; TIGR01382 1427342014079 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 1427342014080 conserved cys residue [active] 1427342014081 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 1427342014082 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1427342014083 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 1427342014084 PLD-like domain; Region: PLDc_2; pfam13091 1427342014085 putative active site [active] 1427342014086 catalytic site [active] 1427342014087 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 1427342014088 PLD-like domain; Region: PLDc_2; pfam13091 1427342014089 putative active site [active] 1427342014090 catalytic site [active] 1427342014091 YceI-like domain; Region: YceI; pfam04264 1427342014092 Transcriptional regulator [Transcription]; Region: IclR; COG1414 1427342014093 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 1427342014094 amidase; Provisional; Region: PRK07486 1427342014095 Amidase; Region: Amidase; pfam01425 1427342014096 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342014097 metabolite-proton symporter; Region: 2A0106; TIGR00883 1427342014098 putative substrate translocation pore; other site 1427342014099 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1427342014100 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 1427342014101 metal binding site [ion binding]; metal-binding site 1427342014102 putative dimer interface [polypeptide binding]; other site 1427342014103 YceI-like domain; Region: YceI; pfam04264 1427342014104 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342014105 Beta-lactamase; Region: Beta-lactamase; pfam00144 1427342014106 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 1427342014107 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1427342014108 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342014109 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342014110 active site 1427342014111 Putative hemolysin [General function prediction only]; Region: COG3176 1427342014112 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1427342014113 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1427342014114 putative acyl-acceptor binding pocket; other site 1427342014115 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342014116 Ligand Binding Site [chemical binding]; other site 1427342014117 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342014118 Ligand Binding Site [chemical binding]; other site 1427342014119 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3124 1427342014120 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342014121 dimerization interface [polypeptide binding]; other site 1427342014122 putative DNA binding site [nucleotide binding]; other site 1427342014123 putative Zn2+ binding site [ion binding]; other site 1427342014124 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342014125 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342014126 putative substrate translocation pore; other site 1427342014127 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342014128 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 1427342014129 FMN binding site [chemical binding]; other site 1427342014130 active site 1427342014131 substrate binding site [chemical binding]; other site 1427342014132 catalytic residue [active] 1427342014133 FeoC like transcriptional regulator; Region: FeoC; cl17677 1427342014134 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 1427342014135 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1427342014136 G1 box; other site 1427342014137 GTP/Mg2+ binding site [chemical binding]; other site 1427342014138 Switch I region; other site 1427342014139 G2 box; other site 1427342014140 G3 box; other site 1427342014141 Switch II region; other site 1427342014142 G4 box; other site 1427342014143 G5 box; other site 1427342014144 Nucleoside recognition; Region: Gate; pfam07670 1427342014145 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1427342014146 Nucleoside recognition; Region: Gate; pfam07670 1427342014147 ferrous iron transport protein A; Reviewed; Region: feoA; PRK09555 1427342014148 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 1427342014149 oligomer interface [polypeptide binding]; other site 1427342014150 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1427342014151 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342014152 NAD(P) binding site [chemical binding]; other site 1427342014153 active site 1427342014154 Uncharacterized conserved protein [Function unknown]; Region: COG3268 1427342014155 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342014156 NAD(P) binding site [chemical binding]; other site 1427342014157 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 1427342014158 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342014159 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342014160 dimerization interface [polypeptide binding]; other site 1427342014161 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3602 1427342014162 ACT domain; Region: ACT_3; pfam10000 1427342014163 Lysine efflux permease [General function prediction only]; Region: COG1279 1427342014164 superoxide dismutase; Provisional; Region: PRK10543 1427342014165 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1427342014166 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1427342014167 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342014168 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342014169 metal binding site [ion binding]; metal-binding site 1427342014170 active site 1427342014171 I-site; other site 1427342014172 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342014173 E3 Ubiquitin ligase; Region: GIDE; pfam12483 1427342014174 LemA family; Region: LemA; pfam04011 1427342014175 Uncharacterized iron-regulated protein [Inorganic ion transport and metabolism]; Region: IrpA; COG3487 1427342014176 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 1427342014177 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 1427342014178 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG3489 1427342014179 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3490 1427342014180 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342014181 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342014182 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342014183 multidrug efflux protein; Reviewed; Region: PRK09579 1427342014184 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342014185 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 1427342014186 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 1427342014187 active site 1427342014188 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 1427342014189 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342014190 S-adenosylmethionine binding site [chemical binding]; other site 1427342014191 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342014192 HAMP domain; Region: HAMP; pfam00672 1427342014193 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342014194 dimer interface [polypeptide binding]; other site 1427342014195 phosphorylation site [posttranslational modification] 1427342014196 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342014197 ATP binding site [chemical binding]; other site 1427342014198 Mg2+ binding site [ion binding]; other site 1427342014199 G-X-G motif; other site 1427342014200 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1427342014201 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342014202 active site 1427342014203 phosphorylation site [posttranslational modification] 1427342014204 intermolecular recognition site; other site 1427342014205 dimerization interface [polypeptide binding]; other site 1427342014206 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342014207 DNA binding site [nucleotide binding] 1427342014208 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 1427342014209 active site 1427342014210 chromosome condensation membrane protein; Provisional; Region: PRK14196 1427342014211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4318 1427342014212 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1427342014213 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 1427342014214 ring oligomerisation interface [polypeptide binding]; other site 1427342014215 ATP/Mg binding site [chemical binding]; other site 1427342014216 stacking interactions; other site 1427342014217 hinge regions; other site 1427342014218 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 1427342014219 oligomerisation interface [polypeptide binding]; other site 1427342014220 mobile loop; other site 1427342014221 roof hairpin; other site 1427342014222 phage T7 F exclusion suppressor FxsA; Reviewed; Region: fxsA; PRK11463 1427342014223 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 1427342014224 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 1427342014225 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 1427342014226 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 1427342014227 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342014228 NAD(P) binding site [chemical binding]; other site 1427342014229 active site 1427342014230 Protein of unknown function, DUF481; Region: DUF481; pfam04338 1427342014231 Protein of unknown function, DUF481; Region: DUF481; pfam04338 1427342014232 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1427342014233 DNA binding site [nucleotide binding] 1427342014234 active site 1427342014235 AmpG-like permease; Region: 2A0125; TIGR00901 1427342014236 muropeptide transporter; Validated; Region: ampG; cl17669 1427342014237 mechanosensitive channel MscS; Provisional; Region: PRK10334 1427342014238 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342014239 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 1427342014240 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 1427342014241 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342014242 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342014243 active site 1427342014244 phosphorylation site [posttranslational modification] 1427342014245 intermolecular recognition site; other site 1427342014246 dimerization interface [polypeptide binding]; other site 1427342014247 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 1427342014248 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 1427342014249 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 1427342014250 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 1427342014251 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342014252 dimerization interface [polypeptide binding]; other site 1427342014253 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 1427342014254 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342014255 putative active site [active] 1427342014256 heme pocket [chemical binding]; other site 1427342014257 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342014258 dimer interface [polypeptide binding]; other site 1427342014259 phosphorylation site [posttranslational modification] 1427342014260 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342014261 ATP binding site [chemical binding]; other site 1427342014262 Mg2+ binding site [ion binding]; other site 1427342014263 G-X-G motif; other site 1427342014264 cob(I)alamin adenosyltransferase [Coenzyme transport and metabolism]; Region: COG2096 1427342014265 hypothetical protein; Provisional; Region: PRK08999 1427342014266 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 1427342014267 active site 1427342014268 8-oxo-dGMP binding site [chemical binding]; other site 1427342014269 nudix motif; other site 1427342014270 metal binding site [ion binding]; metal-binding site 1427342014271 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 1427342014272 thiamine phosphate binding site [chemical binding]; other site 1427342014273 active site 1427342014274 pyrophosphate binding site [ion binding]; other site 1427342014275 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 1427342014276 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1427342014277 putative C-terminal domain interface [polypeptide binding]; other site 1427342014278 putative GSH binding site (G-site) [chemical binding]; other site 1427342014279 putative dimer interface [polypeptide binding]; other site 1427342014280 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 1427342014281 putative N-terminal domain interface [polypeptide binding]; other site 1427342014282 putative dimer interface [polypeptide binding]; other site 1427342014283 putative substrate binding pocket (H-site) [chemical binding]; other site 1427342014284 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 1427342014285 heterotetramer interface [polypeptide binding]; other site 1427342014286 active site pocket [active] 1427342014287 cleavage site 1427342014288 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK13103 1427342014289 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 1427342014290 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1427342014291 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 1427342014292 nucleotide binding region [chemical binding]; other site 1427342014293 ATP-binding site [chemical binding]; other site 1427342014294 SEC-C motif; Region: SEC-C; pfam02810 1427342014295 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1427342014296 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342014297 Protein of unknown function (DUF721); Region: DUF721; cl02324 1427342014298 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1427342014299 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1427342014300 cell division protein FtsZ; Validated; Region: PRK09330 1427342014301 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 1427342014302 nucleotide binding site [chemical binding]; other site 1427342014303 SulA interaction site; other site 1427342014304 cell division protein FtsA; Region: ftsA; TIGR01174 1427342014305 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1427342014306 nucleotide binding site [chemical binding]; other site 1427342014307 Cell division protein FtsA; Region: FtsA; pfam14450 1427342014308 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1427342014309 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1427342014310 Cell division protein FtsQ; Region: FtsQ; pfam03799 1427342014311 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1427342014312 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1427342014313 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342014314 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1427342014315 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1427342014316 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342014317 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1427342014318 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1427342014319 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 1427342014320 active site 1427342014321 homodimer interface [polypeptide binding]; other site 1427342014322 cell division protein FtsW; Region: ftsW; TIGR02614 1427342014323 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 1427342014324 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342014325 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342014326 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1427342014327 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 1427342014328 Mg++ binding site [ion binding]; other site 1427342014329 putative catalytic motif [active] 1427342014330 putative substrate binding site [chemical binding]; other site 1427342014331 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1427342014332 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 1427342014333 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342014334 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1427342014335 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1427342014336 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1427342014337 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1427342014338 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1427342014339 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 1427342014340 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1427342014341 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1427342014342 Cell division protein [Cell division and chromosome partitioning]; Region: FtsL; COG3116 1427342014343 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1427342014344 MraW methylase family; Region: Methyltransf_5; pfam01795 1427342014345 cell division protein MraZ; Reviewed; Region: PRK00326 1427342014346 MraZ protein; Region: MraZ; pfam02381 1427342014347 Predicted methyltransferases [General function prediction only]; Region: COG0313 1427342014348 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1427342014349 putative SAM binding site [chemical binding]; other site 1427342014350 putative homodimer interface [polypeptide binding]; other site 1427342014351 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 1427342014352 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1427342014353 putative ligand binding site [chemical binding]; other site 1427342014354 hypothetical protein; Reviewed; Region: PRK12497 1427342014355 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 1427342014356 dimer interface [polypeptide binding]; other site 1427342014357 active site 1427342014358 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1427342014359 BON domain; Region: BON; pfam04972 1427342014360 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 1427342014361 stringent starvation protein A; Provisional; Region: sspA; PRK09481 1427342014362 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 1427342014363 C-terminal domain interface [polypeptide binding]; other site 1427342014364 putative GSH binding site (G-site) [chemical binding]; other site 1427342014365 dimer interface [polypeptide binding]; other site 1427342014366 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 1427342014367 dimer interface [polypeptide binding]; other site 1427342014368 N-terminal domain interface [polypeptide binding]; other site 1427342014369 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 1427342014370 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 1427342014371 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 1427342014372 Qi binding site; other site 1427342014373 intrachain domain interface; other site 1427342014374 interchain domain interface [polypeptide binding]; other site 1427342014375 heme bH binding site [chemical binding]; other site 1427342014376 heme bL binding site [chemical binding]; other site 1427342014377 Qo binding site; other site 1427342014378 interchain domain interface [polypeptide binding]; other site 1427342014379 intrachain domain interface; other site 1427342014380 Qi binding site; other site 1427342014381 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 1427342014382 Qo binding site; other site 1427342014383 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1427342014384 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 1427342014385 [2Fe-2S] cluster binding site [ion binding]; other site 1427342014386 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1427342014387 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 1427342014388 23S rRNA interface [nucleotide binding]; other site 1427342014389 L3 interface [polypeptide binding]; other site 1427342014390 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342014391 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342014392 active site 1427342014393 catalytic tetrad [active] 1427342014394 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342014395 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342014396 active site 1427342014397 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 1427342014398 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 1427342014399 conserved cys residue [active] 1427342014400 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342014401 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342014402 Predicted ATPase [General function prediction only]; Region: COG1485 1427342014403 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 1427342014404 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1427342014405 active site 1427342014406 HIGH motif; other site 1427342014407 dimer interface [polypeptide binding]; other site 1427342014408 KMSKS motif; other site 1427342014409 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1427342014410 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3105 1427342014411 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 1427342014412 Uncharacterized conserved small protein [Function unknown]; Region: COG5639 1427342014413 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1427342014414 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1427342014415 VirB7 interaction site; other site 1427342014416 conjugal transfer protein TrbF; Provisional; Region: PRK13872 1427342014417 conjugal transfer protein TrbL; Provisional; Region: PRK13875 1427342014418 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1427342014419 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 1427342014420 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 1427342014421 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 1427342014422 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1427342014423 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342014424 Walker A motif; other site 1427342014425 ATP binding site [chemical binding]; other site 1427342014426 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 1427342014427 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 1427342014428 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1427342014429 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 1427342014430 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1427342014431 ATP binding site [chemical binding]; other site 1427342014432 Walker A motif; other site 1427342014433 hexamer interface [polypeptide binding]; other site 1427342014434 Walker B motif; other site 1427342014435 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 1427342014436 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 1427342014437 Walker A motif; other site 1427342014438 ATP binding site [chemical binding]; other site 1427342014439 Walker B motif; other site 1427342014440 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 1427342014441 Transposase; Region: DDE_Tnp_ISL3; pfam01610 1427342014442 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 1427342014443 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 1427342014444 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 1427342014445 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 1427342014446 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 1427342014447 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 1427342014448 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 1427342014449 Transposase domain (DUF772); Region: DUF772; pfam05598 1427342014450 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 1427342014451 DDE superfamily endonuclease; Region: DDE_4; cl17710 1427342014452 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 1427342014453 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342014454 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342014455 dimerization interface [polypeptide binding]; other site 1427342014456 substrate binding pocket [chemical binding]; other site 1427342014457 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1427342014458 NAD(P) binding site [chemical binding]; other site 1427342014459 catalytic residues [active] 1427342014460 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 1427342014461 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 1427342014462 dimer interface [polypeptide binding]; other site 1427342014463 acyl-activating enzyme (AAE) consensus motif; other site 1427342014464 putative active site [active] 1427342014465 AMP binding site [chemical binding]; other site 1427342014466 putative CoA binding site [chemical binding]; other site 1427342014467 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 1427342014468 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342014469 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342014470 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342014471 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 1427342014472 catalytic loop [active] 1427342014473 iron binding site [ion binding]; other site 1427342014474 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD...; Region: oxygenase_e_transfer_subunit; cd06213 1427342014475 FAD binding pocket [chemical binding]; other site 1427342014476 FAD binding motif [chemical binding]; other site 1427342014477 phosphate binding motif [ion binding]; other site 1427342014478 beta-alpha-beta structure motif; other site 1427342014479 NAD binding pocket [chemical binding]; other site 1427342014480 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 1427342014481 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1427342014482 Di-iron ligands [ion binding]; other site 1427342014483 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 1427342014484 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 1427342014485 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 1427342014486 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 1427342014487 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 1427342014488 ParA-like protein; Provisional; Region: PHA02518 1427342014489 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342014490 P-loop; other site 1427342014491 Magnesium ion binding site [ion binding]; other site 1427342014492 Replication initiator protein A; Region: RPA; pfam10134 1427342014493 Helix-turn-helix domain; Region: HTH_17; cl17695 1427342014494 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 1427342014495 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 1427342014496 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1427342014497 sequence-specific DNA binding site [nucleotide binding]; other site 1427342014498 salt bridge; other site 1427342014499 Uncharacterized conserved protein [Function unknown]; Region: COG5489 1427342014500 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342014501 Coenzyme A binding pocket [chemical binding]; other site 1427342014502 ParB-like nuclease domain; Region: ParB; smart00470 1427342014503 Domain of unknown function (DUF932); Region: DUF932; pfam06067 1427342014504 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 1427342014505 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1427342014506 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1427342014507 Prokaryotic E2 family A; Region: Prok-E2_A; pfam14457 1427342014508 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 1427342014509 ATP binding site [chemical binding]; other site 1427342014510 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 1427342014511 WYL domain; Region: WYL; pfam13280 1427342014512 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1427342014513 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1427342014514 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342014515 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 1427342014516 active site 1427342014517 Int/Topo IB signature motif; other site 1427342014518 DNA binding site [nucleotide binding] 1427342014519 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 1427342014520 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 1427342014521 CysD dimerization site [polypeptide binding]; other site 1427342014522 G1 box; other site 1427342014523 putative GEF interaction site [polypeptide binding]; other site 1427342014524 GTP/Mg2+ binding site [chemical binding]; other site 1427342014525 Switch I region; other site 1427342014526 G2 box; other site 1427342014527 G3 box; other site 1427342014528 Switch II region; other site 1427342014529 G4 box; other site 1427342014530 G5 box; other site 1427342014531 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 1427342014532 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 1427342014533 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 1427342014534 ligand-binding site [chemical binding]; other site 1427342014535 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 1427342014536 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 1427342014537 Active Sites [active] 1427342014538 Transglycosylase SLT domain; Region: SLT_2; pfam13406 1427342014539 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 1427342014540 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1427342014541 catalytic residue [active] 1427342014542 Uncharacterized conserved protein [Function unknown]; Region: COG0327 1427342014543 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 1427342014544 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1427342014545 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 1427342014546 protein binding site [polypeptide binding]; other site 1427342014547 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 1427342014548 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342014549 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342014550 homodimer interface [polypeptide binding]; other site 1427342014551 catalytic residue [active] 1427342014552 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 1427342014553 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 1427342014554 NAD binding site [chemical binding]; other site 1427342014555 dimerization interface [polypeptide binding]; other site 1427342014556 product binding site; other site 1427342014557 substrate binding site [chemical binding]; other site 1427342014558 zinc binding site [ion binding]; other site 1427342014559 catalytic residues [active] 1427342014560 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 1427342014561 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 1427342014562 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1427342014563 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 1427342014564 hinge; other site 1427342014565 active site 1427342014566 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 1427342014567 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 1427342014568 anti sigma factor interaction site; other site 1427342014569 regulatory phosphorylation site [posttranslational modification]; other site 1427342014570 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1427342014571 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1427342014572 mce related protein; Region: MCE; pfam02470 1427342014573 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1427342014574 conserved hypothetical integral membrane protein; Region: TIGR00056 1427342014575 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1427342014576 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 1427342014577 Walker A/P-loop; other site 1427342014578 ATP binding site [chemical binding]; other site 1427342014579 Q-loop/lid; other site 1427342014580 ABC transporter signature motif; other site 1427342014581 Walker B; other site 1427342014582 D-loop; other site 1427342014583 H-loop/switch region; other site 1427342014584 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1427342014585 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 1427342014586 putative active site [active] 1427342014587 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 1427342014588 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 1427342014589 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 1427342014590 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 1427342014591 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 1427342014592 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 1427342014593 OstA-like protein; Region: OstA; pfam03968 1427342014594 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1427342014595 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 1427342014596 Walker A/P-loop; other site 1427342014597 ATP binding site [chemical binding]; other site 1427342014598 Q-loop/lid; other site 1427342014599 ABC transporter signature motif; other site 1427342014600 Walker B; other site 1427342014601 D-loop; other site 1427342014602 H-loop/switch region; other site 1427342014603 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 1427342014604 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 1427342014605 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 1427342014606 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 1427342014607 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 1427342014608 30S subunit binding site; other site 1427342014609 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 1427342014610 active site 1427342014611 phosphorylation site [posttranslational modification] 1427342014612 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 1427342014613 AAA domain; Region: AAA_18; pfam13238 1427342014614 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 1427342014615 dimerization domain swap beta strand [polypeptide binding]; other site 1427342014616 regulatory protein interface [polypeptide binding]; other site 1427342014617 active site 1427342014618 regulatory phosphorylation site [posttranslational modification]; other site 1427342014619 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 1427342014620 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1427342014621 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1427342014622 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1427342014623 Protein of unknown function (DUF2753); Region: DUF2753; pfam10952 1427342014624 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1427342014625 Class II fumarases; Region: Fumarase_classII; cd01362 1427342014626 active site 1427342014627 tetramer interface [polypeptide binding]; other site 1427342014628 peptidase PmbA; Provisional; Region: PRK11040 1427342014629 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3028 1427342014630 protease TldD; Provisional; Region: tldD; PRK10735 1427342014631 nitrilase; Region: PLN02798 1427342014632 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 1427342014633 putative active site [active] 1427342014634 catalytic triad [active] 1427342014635 dimer interface [polypeptide binding]; other site 1427342014636 Predicted membrane protein [Function unknown]; Region: COG3164 1427342014637 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1427342014638 ribonuclease G; Provisional; Region: PRK11712 1427342014639 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 1427342014640 homodimer interface [polypeptide binding]; other site 1427342014641 oligonucleotide binding site [chemical binding]; other site 1427342014642 Maf-like protein; Region: Maf; pfam02545 1427342014643 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 1427342014644 active site 1427342014645 dimer interface [polypeptide binding]; other site 1427342014646 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 1427342014647 rod shape-determining protein MreC; Provisional; Region: PRK13922 1427342014648 rod shape-determining protein MreC; Region: MreC; pfam04085 1427342014649 rod shape-determining protein MreB; Provisional; Region: PRK13927 1427342014650 MreB and similar proteins; Region: MreB_like; cd10225 1427342014651 nucleotide binding site [chemical binding]; other site 1427342014652 Mg binding site [ion binding]; other site 1427342014653 putative protofilament interaction site [polypeptide binding]; other site 1427342014654 RodZ interaction site [polypeptide binding]; other site 1427342014655 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1427342014656 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1427342014657 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1427342014658 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1427342014659 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1427342014660 GatB domain; Region: GatB_Yqey; smart00845 1427342014661 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1427342014662 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1427342014663 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 1427342014664 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 1427342014665 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cl17565 1427342014666 putative metal binding site [ion binding]; other site 1427342014667 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 1427342014668 Predicted secreted protein [Function unknown]; Region: COG5445 1427342014669 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 1427342014670 Predicted secreted protein [Function unknown]; Region: COG5445 1427342014671 Stage II sporulation protein; Region: SpoIID; pfam08486 1427342014672 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 1427342014673 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 1427342014674 MG2 domain; Region: A2M_N; pfam01835 1427342014675 Alpha-2-macroglobulin family; Region: A2M; pfam00207 1427342014676 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 1427342014677 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3234 1427342014678 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4685 1427342014679 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 1427342014680 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 1427342014681 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 1427342014682 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342014683 active site 1427342014684 phosphorylation site [posttranslational modification] 1427342014685 intermolecular recognition site; other site 1427342014686 dimerization interface [polypeptide binding]; other site 1427342014687 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342014688 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342014689 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342014690 phosphorylation site [posttranslational modification] 1427342014691 dimer interface [polypeptide binding]; other site 1427342014692 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 1427342014693 ATP binding site [chemical binding]; other site 1427342014694 G-X-G motif; other site 1427342014695 Predicted periplasmic/secreted protein [Function unknown]; Region: COG3471 1427342014696 Uncharacterized conserved protein [Function unknown]; Region: COG2968 1427342014697 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1427342014698 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1427342014699 peptide binding site [polypeptide binding]; other site 1427342014700 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1427342014701 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1427342014702 peptide binding site [polypeptide binding]; other site 1427342014703 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1427342014704 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1427342014705 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cl00279 1427342014706 active site 1427342014707 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342014708 non-specific DNA binding site [nucleotide binding]; other site 1427342014709 salt bridge; other site 1427342014710 sequence-specific DNA binding site [nucleotide binding]; other site 1427342014711 Cupin domain; Region: Cupin_2; pfam07883 1427342014712 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1427342014713 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1427342014714 peptide binding site [polypeptide binding]; other site 1427342014715 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342014716 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1427342014717 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1427342014718 peptide binding site [polypeptide binding]; other site 1427342014719 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1427342014720 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342014721 dimer interface [polypeptide binding]; other site 1427342014722 conserved gate region; other site 1427342014723 putative PBP binding loops; other site 1427342014724 ABC-ATPase subunit interface; other site 1427342014725 dipeptide transporter; Provisional; Region: PRK10913 1427342014726 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 1427342014727 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342014728 putative PBP binding loops; other site 1427342014729 dimer interface [polypeptide binding]; other site 1427342014730 ABC-ATPase subunit interface; other site 1427342014731 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 1427342014732 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342014733 Walker A/P-loop; other site 1427342014734 ATP binding site [chemical binding]; other site 1427342014735 Q-loop/lid; other site 1427342014736 ABC transporter signature motif; other site 1427342014737 Walker B; other site 1427342014738 D-loop; other site 1427342014739 H-loop/switch region; other site 1427342014740 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1427342014741 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 1427342014742 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1427342014743 Walker A/P-loop; other site 1427342014744 ATP binding site [chemical binding]; other site 1427342014745 Q-loop/lid; other site 1427342014746 ABC transporter signature motif; other site 1427342014747 Walker B; other site 1427342014748 D-loop; other site 1427342014749 H-loop/switch region; other site 1427342014750 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 1427342014751 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342014752 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342014753 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342014754 putative DNA binding site [nucleotide binding]; other site 1427342014755 putative Zn2+ binding site [ion binding]; other site 1427342014756 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342014757 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 1427342014758 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1427342014759 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 1427342014760 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 1427342014761 putative active site [active] 1427342014762 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 1427342014763 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 1427342014764 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 1427342014765 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 1427342014766 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 1427342014767 Flavodoxin; Region: Flavodoxin_1; pfam00258 1427342014768 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 1427342014769 FAD binding pocket [chemical binding]; other site 1427342014770 FAD binding motif [chemical binding]; other site 1427342014771 catalytic residues [active] 1427342014772 NAD binding pocket [chemical binding]; other site 1427342014773 phosphate binding motif [ion binding]; other site 1427342014774 beta-alpha-beta structure motif; other site 1427342014775 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 1427342014776 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342014777 N-terminal plug; other site 1427342014778 ligand-binding site [chemical binding]; other site 1427342014779 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 1427342014780 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1427342014781 Sel1-like repeats; Region: SEL1; smart00671 1427342014782 Sel1-like repeats; Region: SEL1; smart00671 1427342014783 hypothetical protein; Provisional; Region: PRK10649 1427342014784 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1427342014785 Sulfatase; Region: Sulfatase; pfam00884 1427342014786 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 1427342014787 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342014788 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 1427342014789 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 1427342014790 dimer interface [polypeptide binding]; other site 1427342014791 active site 1427342014792 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342014793 catalytic residues [active] 1427342014794 substrate binding site [chemical binding]; other site 1427342014795 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342014796 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342014797 dimerization interface [polypeptide binding]; other site 1427342014798 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342014799 dimer interface [polypeptide binding]; other site 1427342014800 putative CheW interface [polypeptide binding]; other site 1427342014801 Membrane protein required for beta-lactamase induction [Defense mechanisms]; Region: AmpE; cl17896 1427342014802 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1427342014803 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1427342014804 amidase catalytic site [active] 1427342014805 Zn binding residues [ion binding]; other site 1427342014806 substrate binding site [chemical binding]; other site 1427342014807 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 1427342014808 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05742 1427342014809 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 1427342014810 dimerization interface [polypeptide binding]; other site 1427342014811 active site 1427342014812 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 1427342014813 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 1427342014814 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 1427342014815 Walker A motif; other site 1427342014816 ATP binding site [chemical binding]; other site 1427342014817 Walker B motif; other site 1427342014818 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 1427342014819 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342014820 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1427342014821 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 1427342014822 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 1427342014823 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 1427342014824 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1427342014825 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 1427342014826 CoA-binding site [chemical binding]; other site 1427342014827 ATP-binding [chemical binding]; other site 1427342014828 DNA gyrase inhibitor; Reviewed; Region: PRK00418 1427342014829 Predicted membrane protein [Function unknown]; Region: COG3235 1427342014830 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 1427342014831 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1427342014832 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342014833 Coenzyme A binding pocket [chemical binding]; other site 1427342014834 Protein of unknown function (DUF1780); Region: DUF1780; pfam08682 1427342014835 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 1427342014836 MOSC domain; Region: MOSC; pfam03473 1427342014837 Protein of unknown function (DUF3094); Region: DUF3094; pfam11293 1427342014838 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 1427342014839 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342014840 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 1427342014841 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 1427342014842 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 1427342014843 Surface antigen; Region: Bac_surface_Ag; pfam01103 1427342014844 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 1427342014845 haemagglutination activity domain; Region: Haemagg_act; pfam05860 1427342014846 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1427342014847 Clp amino terminal domain; Region: Clp_N; pfam02861 1427342014848 Clp amino terminal domain; Region: Clp_N; pfam02861 1427342014849 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342014850 Walker A motif; other site 1427342014851 ATP binding site [chemical binding]; other site 1427342014852 Walker B motif; other site 1427342014853 arginine finger; other site 1427342014854 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342014855 Walker A motif; other site 1427342014856 ATP binding site [chemical binding]; other site 1427342014857 Walker B motif; other site 1427342014858 arginine finger; other site 1427342014859 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1427342014860 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 1427342014861 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1427342014862 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 1427342014863 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342014864 RNA binding surface [nucleotide binding]; other site 1427342014865 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1427342014866 active site 1427342014867 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 1427342014868 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 1427342014869 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342014870 dimer interface [polypeptide binding]; other site 1427342014871 phosphorylation site [posttranslational modification] 1427342014872 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342014873 ATP binding site [chemical binding]; other site 1427342014874 Mg2+ binding site [ion binding]; other site 1427342014875 G-X-G motif; other site 1427342014876 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342014877 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342014878 active site 1427342014879 phosphorylation site [posttranslational modification] 1427342014880 intermolecular recognition site; other site 1427342014881 dimerization interface [polypeptide binding]; other site 1427342014882 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342014883 Walker A motif; other site 1427342014884 ATP binding site [chemical binding]; other site 1427342014885 Walker B motif; other site 1427342014886 arginine finger; other site 1427342014887 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342014888 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 1427342014889 Type II transport protein GspH; Region: GspH; pfam12019 1427342014890 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1427342014891 Type II transport protein GspH; Region: GspH; pfam12019 1427342014892 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 1427342014893 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 1427342014894 PilX N-terminal; Region: PilX_N; pfam14341 1427342014895 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 1427342014896 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 1427342014897 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 1427342014898 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 1427342014899 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 1427342014900 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 1427342014901 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342014902 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1427342014903 lipoprotein signal peptidase; Provisional; Region: PRK14787 1427342014904 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 1427342014905 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1427342014906 active site 1427342014907 HIGH motif; other site 1427342014908 nucleotide binding site [chemical binding]; other site 1427342014909 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1427342014910 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1427342014911 active site 1427342014912 KMSKS motif; other site 1427342014913 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 1427342014914 tRNA binding surface [nucleotide binding]; other site 1427342014915 anticodon binding site; other site 1427342014916 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1427342014917 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 1427342014918 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 1427342014919 active site 1427342014920 Riboflavin kinase; Region: Flavokinase; pfam01687 1427342014921 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1427342014922 MviN-like protein; Region: MVIN; pfam03023 1427342014923 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1427342014924 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 1427342014925 CreA protein; Region: CreA; pfam05981 1427342014926 gamma-glutamyl kinase; Provisional; Region: PRK05429 1427342014927 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 1427342014928 nucleotide binding site [chemical binding]; other site 1427342014929 homotetrameric interface [polypeptide binding]; other site 1427342014930 putative phosphate binding site [ion binding]; other site 1427342014931 putative allosteric binding site; other site 1427342014932 PUA domain; Region: PUA; pfam01472 1427342014933 GTPase CgtA; Reviewed; Region: obgE; PRK12298 1427342014934 GTP1/OBG; Region: GTP1_OBG; pfam01018 1427342014935 Obg GTPase; Region: Obg; cd01898 1427342014936 G1 box; other site 1427342014937 GTP/Mg2+ binding site [chemical binding]; other site 1427342014938 Switch I region; other site 1427342014939 G2 box; other site 1427342014940 G3 box; other site 1427342014941 Switch II region; other site 1427342014942 G4 box; other site 1427342014943 G5 box; other site 1427342014944 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1427342014945 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1427342014946 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1427342014947 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1427342014948 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1427342014949 substrate binding pocket [chemical binding]; other site 1427342014950 chain length determination region; other site 1427342014951 substrate-Mg2+ binding site; other site 1427342014952 catalytic residues [active] 1427342014953 aspartate-rich region 1; other site 1427342014954 active site lid residues [active] 1427342014955 aspartate-rich region 2; other site 1427342014956 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342014957 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342014958 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342014959 Cytochrome c [Energy production and conversion]; Region: COG3258 1427342014960 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342014961 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 1427342014962 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 1427342014963 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342014964 hypothetical protein; Provisional; Region: PRK05208 1427342014965 methane monooxygenase/ammonia monooxygenase, subunit A; Region: CH4_NH3mon_ox_A; TIGR03080 1427342014966 AAA domain; Region: AAA_32; pfam13654 1427342014967 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1427342014968 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 1427342014969 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 1427342014970 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 1427342014971 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3236 1427342014972 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 1427342014973 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 1427342014974 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342014975 Walker A motif; other site 1427342014976 ATP binding site [chemical binding]; other site 1427342014977 Walker B motif; other site 1427342014978 arginine finger; other site 1427342014979 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1427342014980 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 1427342014981 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 1427342014982 hypothetical protein; Reviewed; Region: PRK09588 1427342014983 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1427342014984 active site 1427342014985 NTP binding site [chemical binding]; other site 1427342014986 metal binding triad [ion binding]; metal-binding site 1427342014987 antibiotic binding site [chemical binding]; other site 1427342014988 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 1427342014989 RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine...; Region: RNA_Cyclase_Class_II; cd00874 1427342014990 putative active site [active] 1427342014991 adenylation catalytic residue [active] 1427342014992 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 1427342014993 glutamate dehydrogenase; Provisional; Region: PRK09414 1427342014994 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1427342014995 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 1427342014996 NAD(P) binding site [chemical binding]; other site 1427342014997 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 1427342014998 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342014999 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342015000 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342015001 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1427342015002 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1427342015003 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1427342015004 FtsX-like permease family; Region: FtsX; pfam02687 1427342015005 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1427342015006 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1427342015007 Walker A/P-loop; other site 1427342015008 ATP binding site [chemical binding]; other site 1427342015009 Q-loop/lid; other site 1427342015010 ABC transporter signature motif; other site 1427342015011 Walker B; other site 1427342015012 D-loop; other site 1427342015013 H-loop/switch region; other site 1427342015014 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1427342015015 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342015016 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342015017 ABC transporter; Region: ABC_tran_2; pfam12848 1427342015018 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342015019 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342015020 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342015021 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 1427342015022 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 1427342015023 Protein export membrane protein; Region: SecD_SecF; cl14618 1427342015024 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1427342015025 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342015026 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342015027 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342015028 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cl17402 1427342015029 PAS domain; Region: PAS_9; pfam13426 1427342015030 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342015031 PAS fold; Region: PAS_3; pfam08447 1427342015032 putative active site [active] 1427342015033 heme pocket [chemical binding]; other site 1427342015034 PAS domain; Region: PAS_9; pfam13426 1427342015035 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 1427342015036 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342015037 PAS domain; Region: PAS_9; pfam13426 1427342015038 putative active site [active] 1427342015039 heme pocket [chemical binding]; other site 1427342015040 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342015041 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342015042 metal binding site [ion binding]; metal-binding site 1427342015043 active site 1427342015044 I-site; other site 1427342015045 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342015046 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1427342015047 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 1427342015048 dimer interface [polypeptide binding]; other site 1427342015049 active site 1427342015050 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1427342015051 folate binding site [chemical binding]; other site 1427342015052 putative GTP-binding protein YjiA; Provisional; Region: PRK11537 1427342015053 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 1427342015054 P-loop, Walker A motif; other site 1427342015055 Base recognition motif; other site 1427342015056 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 1427342015057 Uncharacterized small protein [Function unknown]; Region: COG2879 1427342015058 carbon starvation protein A; Provisional; Region: PRK15015 1427342015059 Carbon starvation protein CstA; Region: CstA; pfam02554 1427342015060 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 1427342015061 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 1427342015062 PilZ domain; Region: PilZ; pfam07238 1427342015063 DNA repair protein RadA; Provisional; Region: PRK11823 1427342015064 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 1427342015065 Walker A motif/ATP binding site; other site 1427342015066 ATP binding site [chemical binding]; other site 1427342015067 Walker B motif; other site 1427342015068 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1427342015069 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 1427342015070 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1427342015071 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1427342015072 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1427342015073 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1427342015074 Clade 1 of the heme-binding enzyme catalase; Region: catalase_clade_1; cd08154 1427342015075 tetramer interface [polypeptide binding]; other site 1427342015076 heme binding pocket [chemical binding]; other site 1427342015077 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 1427342015078 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 1427342015079 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 1427342015080 ferredoxin-NADP reductase; Provisional; Region: PRK10926 1427342015081 FAD binding pocket [chemical binding]; other site 1427342015082 FAD binding motif [chemical binding]; other site 1427342015083 phosphate binding motif [ion binding]; other site 1427342015084 beta-alpha-beta structure motif; other site 1427342015085 NAD binding pocket [chemical binding]; other site 1427342015086 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 1427342015087 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 1427342015088 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 1427342015089 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015090 S-adenosylmethionine binding site [chemical binding]; other site 1427342015091 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 1427342015092 Ligand binding site; other site 1427342015093 metal-binding site 1427342015094 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 1427342015095 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 1427342015096 XdhC Rossmann domain; Region: XdhC_C; pfam13478 1427342015097 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342015098 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342015099 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342015100 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1427342015101 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1427342015102 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342015103 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342015104 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1427342015105 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1427342015106 H+ Antiporter protein; Region: 2A0121; TIGR00900 1427342015107 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 1427342015108 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 1427342015109 haemagglutination activity domain; Region: Haemagg_act; pfam05860 1427342015110 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 1427342015111 glycerate dehydrogenase; Provisional; Region: PRK06487 1427342015112 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 1427342015113 putative ligand binding site [chemical binding]; other site 1427342015114 putative NAD binding site [chemical binding]; other site 1427342015115 catalytic site [active] 1427342015116 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 1427342015117 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 1427342015118 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015119 S-adenosylmethionine binding site [chemical binding]; other site 1427342015120 lysine transporter; Provisional; Region: PRK10836 1427342015121 Predicted membrane protein [Function unknown]; Region: COG2119 1427342015122 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 1427342015123 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 1427342015124 conserved hypothetical protein, steroid delta-isomerase-related; Region: TIGR02096 1427342015125 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 1427342015126 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342015127 NAD(P) binding site [chemical binding]; other site 1427342015128 active site 1427342015129 Peptidase family M48; Region: Peptidase_M48; pfam01435 1427342015130 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342015131 dimerization interface [polypeptide binding]; other site 1427342015132 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342015133 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342015134 dimer interface [polypeptide binding]; other site 1427342015135 putative CheW interface [polypeptide binding]; other site 1427342015136 Uncharacterized conserved protein [Function unknown]; Region: COG2135 1427342015137 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 1427342015138 MgtC family; Region: MgtC; pfam02308 1427342015139 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 1427342015140 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 1427342015141 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 1427342015142 putative acyl-acceptor binding pocket; other site 1427342015143 malate:quinone oxidoreductase; Reviewed; Region: PRK13339 1427342015144 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 1427342015145 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 1427342015146 dimer interface [polypeptide binding]; other site 1427342015147 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342015148 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 1427342015149 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342015150 active site 1427342015151 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342015152 active site 1427342015153 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 1427342015154 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1427342015155 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1427342015156 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1427342015157 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1427342015158 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1427342015159 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 1427342015160 PapC N-terminal domain; Region: PapC_N; pfam13954 1427342015161 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 1427342015162 PapC C-terminal domain; Region: PapC_C; pfam13953 1427342015163 Spore Coat Protein U domain; Region: SCPU; pfam05229 1427342015164 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1427342015165 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342015166 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342015167 putative substrate translocation pore; other site 1427342015168 ferrochelatase; Reviewed; Region: hemH; PRK00035 1427342015169 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 1427342015170 C-terminal domain interface [polypeptide binding]; other site 1427342015171 active site 1427342015172 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 1427342015173 active site 1427342015174 N-terminal domain interface [polypeptide binding]; other site 1427342015175 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 1427342015176 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342015177 NAD(P) binding site [chemical binding]; other site 1427342015178 active site 1427342015179 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 1427342015180 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342015181 Protein of unknown function (DUF523); Region: DUF523; pfam04463 1427342015182 Uncharacterized conserved protein [Function unknown]; Region: COG3272 1427342015183 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 1427342015184 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1427342015185 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 1427342015186 DNA binding residues [nucleotide binding] 1427342015187 B12 binding domain; Region: B12-binding_2; pfam02607 1427342015188 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 1427342015189 DNA photolyase; Region: DNA_photolyase; pfam00875 1427342015190 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 1427342015191 glutamate racemase; Provisional; Region: PRK00865 1427342015192 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 1427342015193 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 1427342015194 ATP binding site [chemical binding]; other site 1427342015195 substrate interface [chemical binding]; other site 1427342015196 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 1427342015197 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015198 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1427342015199 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1427342015200 RF-1 domain; Region: RF-1; pfam00472 1427342015201 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 1427342015202 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 1427342015203 tRNA; other site 1427342015204 putative tRNA binding site [nucleotide binding]; other site 1427342015205 putative NADP binding site [chemical binding]; other site 1427342015206 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 1427342015207 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 1427342015208 TPR motif; other site 1427342015209 binding surface 1427342015210 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342015211 binding surface 1427342015212 TPR motif; other site 1427342015213 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1427342015214 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 1427342015215 binding surface 1427342015216 TPR motif; other site 1427342015217 TPR repeat; Region: TPR_11; pfam13414 1427342015218 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342015219 binding surface 1427342015220 TPR motif; other site 1427342015221 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 1427342015222 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 1427342015223 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1427342015224 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1427342015225 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 1427342015226 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342015227 active site 1427342015228 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1427342015229 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1427342015230 5S rRNA interface [nucleotide binding]; other site 1427342015231 CTC domain interface [polypeptide binding]; other site 1427342015232 L16 interface [polypeptide binding]; other site 1427342015233 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1427342015234 metal binding site [ion binding]; metal-binding site 1427342015235 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 1427342015236 putative active site [active] 1427342015237 GTP-binding protein YchF; Reviewed; Region: PRK09601 1427342015238 YchF GTPase; Region: YchF; cd01900 1427342015239 G1 box; other site 1427342015240 GTP/Mg2+ binding site [chemical binding]; other site 1427342015241 Switch I region; other site 1427342015242 G2 box; other site 1427342015243 Switch II region; other site 1427342015244 G3 box; other site 1427342015245 G4 box; other site 1427342015246 G5 box; other site 1427342015247 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 1427342015248 integrase; Provisional; Region: int; PHA02601 1427342015249 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342015250 active site 1427342015251 DNA binding site [nucleotide binding] 1427342015252 Int/Topo IB signature motif; other site 1427342015253 Zonula occludens toxin [General function prediction only]; Region: Zot; COG4128 1427342015254 putative assembly protein; Region: PHA00350 1427342015255 hypothetical protein; Region: PHA01159 1427342015256 Phage Coat protein B; Region: Phage_Coat_B; pfam05356 1427342015257 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 1427342015258 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342015259 active site 1427342015260 motif I; other site 1427342015261 motif II; other site 1427342015262 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342015263 active site 1427342015264 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1427342015265 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 1427342015266 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342015267 sequence-specific DNA binding site [nucleotide binding]; other site 1427342015268 salt bridge; other site 1427342015269 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 1427342015270 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342015271 N-terminal plug; other site 1427342015272 ligand-binding site [chemical binding]; other site 1427342015273 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 1427342015274 active site clefts [active] 1427342015275 zinc binding site [ion binding]; other site 1427342015276 dimer interface [polypeptide binding]; other site 1427342015277 Dipeptidase [Amino acid transport and metabolism]; Region: PepD; COG4690 1427342015278 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 1427342015279 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342015280 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 1427342015281 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1427342015282 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1427342015283 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342015284 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 1427342015285 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342015286 dimer interface [polypeptide binding]; other site 1427342015287 conserved gate region; other site 1427342015288 putative PBP binding loops; other site 1427342015289 ABC-ATPase subunit interface; other site 1427342015290 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342015291 dimer interface [polypeptide binding]; other site 1427342015292 conserved gate region; other site 1427342015293 putative PBP binding loops; other site 1427342015294 ABC-ATPase subunit interface; other site 1427342015295 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 1427342015296 mce related protein; Region: MCE; pfam02470 1427342015297 mce related protein; Region: MCE; pfam02470 1427342015298 mce related protein; Region: MCE; pfam02470 1427342015299 mce related protein; Region: MCE; pfam02470 1427342015300 mce related protein; Region: MCE; pfam02470 1427342015301 mce related protein; Region: MCE; pfam02470 1427342015302 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 1427342015303 Paraquat-inducible protein A; Region: PqiA; pfam04403 1427342015304 Paraquat-inducible protein A; Region: PqiA; pfam04403 1427342015305 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 1427342015306 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 1427342015307 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 1427342015308 Moco binding site; other site 1427342015309 metal coordination site [ion binding]; other site 1427342015310 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1427342015311 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1427342015312 ketol-acid reductoisomerase; Provisional; Region: PRK05479 1427342015313 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 1427342015314 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 1427342015315 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 1427342015316 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 1427342015317 putative valine binding site [chemical binding]; other site 1427342015318 dimer interface [polypeptide binding]; other site 1427342015319 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 1427342015320 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 1427342015321 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342015322 PYR/PP interface [polypeptide binding]; other site 1427342015323 dimer interface [polypeptide binding]; other site 1427342015324 TPP binding site [chemical binding]; other site 1427342015325 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342015326 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 1427342015327 TPP-binding site [chemical binding]; other site 1427342015328 dimer interface [polypeptide binding]; other site 1427342015329 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 1427342015330 tRNA pseudouridine synthase C; Region: DUF446; cl01187 1427342015331 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342015332 TPR motif; other site 1427342015333 binding surface 1427342015334 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 1427342015335 Transglycosylase; Region: Transgly; pfam00912 1427342015336 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1427342015337 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 1427342015338 Predicted kinase [General function prediction only]; Region: COG0645 1427342015339 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 1427342015340 ATP-binding site [chemical binding]; other site 1427342015341 Gluconate-6-phosphate binding site [chemical binding]; other site 1427342015342 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1427342015343 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1427342015344 TfoX C-terminal domain; Region: TfoX_C; pfam04994 1427342015345 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 1427342015346 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1427342015347 ligand binding site [chemical binding]; other site 1427342015348 flexible hinge region; other site 1427342015349 Uncharacterized iron-regulated protein [Function unknown]; Region: PhuW; COG3016 1427342015350 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 1427342015351 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1427342015352 Walker A/P-loop; other site 1427342015353 ATP binding site [chemical binding]; other site 1427342015354 Q-loop/lid; other site 1427342015355 ABC transporter signature motif; other site 1427342015356 Walker B; other site 1427342015357 D-loop; other site 1427342015358 H-loop/switch region; other site 1427342015359 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1427342015360 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 1427342015361 ABC-ATPase subunit interface; other site 1427342015362 dimer interface [polypeptide binding]; other site 1427342015363 putative PBP binding regions; other site 1427342015364 ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ChuT; COG4558 1427342015365 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 1427342015366 putative hemin binding site; other site 1427342015367 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 1427342015368 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 1427342015369 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 1427342015370 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 1427342015371 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342015372 N-terminal plug; other site 1427342015373 ligand-binding site [chemical binding]; other site 1427342015374 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 1427342015375 iron-sulfur cluster [ion binding]; other site 1427342015376 [2Fe-2S] cluster binding site [ion binding]; other site 1427342015377 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 1427342015378 Predicted metal-binding protein [General function prediction only]; Region: COG3019 1427342015379 aminotransferase; Validated; Region: PRK08175 1427342015380 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342015381 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342015382 homodimer interface [polypeptide binding]; other site 1427342015383 catalytic residue [active] 1427342015384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 1427342015385 Predicted metalloprotease [General function prediction only]; Region: COG2321 1427342015386 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 1427342015387 Preprotein translocase subunit SecD [Intracellular trafficking and secretion]; Region: SecD; COG0342 1427342015388 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1427342015389 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 1427342015390 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 1427342015391 hypothetical protein; Provisional; Region: PRK08960 1427342015392 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342015393 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342015394 homodimer interface [polypeptide binding]; other site 1427342015395 catalytic residue [active] 1427342015396 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1427342015397 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 1427342015398 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 1427342015399 active site 1427342015400 HIGH motif; other site 1427342015401 nucleotide binding site [chemical binding]; other site 1427342015402 KMSKS motif; other site 1427342015403 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 1427342015404 Na binding site [ion binding]; other site 1427342015405 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1427342015406 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 1427342015407 putative active site [active] 1427342015408 heme pocket [chemical binding]; other site 1427342015409 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342015410 dimer interface [polypeptide binding]; other site 1427342015411 phosphorylation site [posttranslational modification] 1427342015412 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342015413 ATP binding site [chemical binding]; other site 1427342015414 Mg2+ binding site [ion binding]; other site 1427342015415 G-X-G motif; other site 1427342015416 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342015417 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015418 active site 1427342015419 phosphorylation site [posttranslational modification] 1427342015420 intermolecular recognition site; other site 1427342015421 dimerization interface [polypeptide binding]; other site 1427342015422 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342015423 Walker A motif; other site 1427342015424 ATP binding site [chemical binding]; other site 1427342015425 Walker B motif; other site 1427342015426 arginine finger; other site 1427342015427 poly(A) polymerase; Region: pcnB; TIGR01942 1427342015428 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1427342015429 active site 1427342015430 NTP binding site [chemical binding]; other site 1427342015431 metal binding triad [ion binding]; metal-binding site 1427342015432 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1427342015433 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 1427342015434 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 1427342015435 catalytic center binding site [active] 1427342015436 ATP binding site [chemical binding]; other site 1427342015437 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 1427342015438 oligomerization interface [polypeptide binding]; other site 1427342015439 active site 1427342015440 metal binding site [ion binding]; metal-binding site 1427342015441 Pantoate-beta-alanine ligase; Region: PanC; cd00560 1427342015442 pantoate--beta-alanine ligase; Region: panC; TIGR00018 1427342015443 active site 1427342015444 ATP-binding site [chemical binding]; other site 1427342015445 pantoate-binding site; other site 1427342015446 HXXH motif; other site 1427342015447 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 1427342015448 tetramerization interface [polypeptide binding]; other site 1427342015449 active site 1427342015450 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 1427342015451 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 1427342015452 active site 1427342015453 dimer interface [polypeptide binding]; other site 1427342015454 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 1427342015455 dimer interface [polypeptide binding]; other site 1427342015456 active site 1427342015457 acetyl-CoA synthetase; Provisional; Region: PRK00174 1427342015458 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 1427342015459 active site 1427342015460 CoA binding site [chemical binding]; other site 1427342015461 acyl-activating enzyme (AAE) consensus motif; other site 1427342015462 AMP binding site [chemical binding]; other site 1427342015463 acetate binding site [chemical binding]; other site 1427342015464 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3662 1427342015465 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 1427342015466 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 1427342015467 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 1427342015468 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1427342015469 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 1427342015470 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 1427342015471 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 1427342015472 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3237 1427342015473 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1427342015474 BON domain; Region: BON; pfam04972 1427342015475 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1427342015476 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1427342015477 RNase E interface [polypeptide binding]; other site 1427342015478 trimer interface [polypeptide binding]; other site 1427342015479 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1427342015480 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1427342015481 RNase E interface [polypeptide binding]; other site 1427342015482 trimer interface [polypeptide binding]; other site 1427342015483 active site 1427342015484 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 1427342015485 putative nucleic acid binding region [nucleotide binding]; other site 1427342015486 G-X-X-G motif; other site 1427342015487 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 1427342015488 RNA binding site [nucleotide binding]; other site 1427342015489 domain interface; other site 1427342015490 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 1427342015491 16S/18S rRNA binding site [nucleotide binding]; other site 1427342015492 S13e-L30e interaction site [polypeptide binding]; other site 1427342015493 25S rRNA binding site [nucleotide binding]; other site 1427342015494 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 1427342015495 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1427342015496 RNA binding site [nucleotide binding]; other site 1427342015497 active site 1427342015498 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 1427342015499 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1427342015500 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 1427342015501 translation initiation factor IF-2; Region: IF-2; TIGR00487 1427342015502 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1427342015503 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1427342015504 G1 box; other site 1427342015505 putative GEF interaction site [polypeptide binding]; other site 1427342015506 GTP/Mg2+ binding site [chemical binding]; other site 1427342015507 Switch I region; other site 1427342015508 G2 box; other site 1427342015509 G3 box; other site 1427342015510 Switch II region; other site 1427342015511 G4 box; other site 1427342015512 G5 box; other site 1427342015513 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 1427342015514 Translation-initiation factor 2; Region: IF-2; pfam11987 1427342015515 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 1427342015516 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1427342015517 NusA N-terminal domain; Region: NusA_N; pfam08529 1427342015518 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 1427342015519 RNA binding site [nucleotide binding]; other site 1427342015520 homodimer interface [polypeptide binding]; other site 1427342015521 NusA-like KH domain; Region: KH_5; pfam13184 1427342015522 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 1427342015523 G-X-X-G motif; other site 1427342015524 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1427342015525 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1427342015526 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1427342015527 Sm and related proteins; Region: Sm_like; cl00259 1427342015528 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1427342015529 putative oligomer interface [polypeptide binding]; other site 1427342015530 putative RNA binding site [nucleotide binding]; other site 1427342015531 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 1427342015532 triosephosphate isomerase; Provisional; Region: PRK14567 1427342015533 substrate binding site [chemical binding]; other site 1427342015534 dimer interface [polypeptide binding]; other site 1427342015535 catalytic triad [active] 1427342015536 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 1427342015537 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 1427342015538 active site 1427342015539 substrate binding site [chemical binding]; other site 1427342015540 metal binding site [ion binding]; metal-binding site 1427342015541 dihydropteroate synthase; Region: DHPS; TIGR01496 1427342015542 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 1427342015543 substrate binding pocket [chemical binding]; other site 1427342015544 dimer interface [polypeptide binding]; other site 1427342015545 inhibitor binding site; inhibition site 1427342015546 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 1427342015547 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342015548 Walker A motif; other site 1427342015549 ATP binding site [chemical binding]; other site 1427342015550 Walker B motif; other site 1427342015551 arginine finger; other site 1427342015552 Peptidase family M41; Region: Peptidase_M41; pfam01434 1427342015553 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1427342015554 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015555 S-adenosylmethionine binding site [chemical binding]; other site 1427342015556 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 1427342015557 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1427342015558 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1427342015559 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1427342015560 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 1427342015561 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342015562 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1427342015563 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 1427342015564 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342015565 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1427342015566 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 1427342015567 IMP binding site; other site 1427342015568 dimer interface [polypeptide binding]; other site 1427342015569 interdomain contacts; other site 1427342015570 partial ornithine binding site; other site 1427342015571 leucine export protein LeuE; Provisional; Region: PRK10958 1427342015572 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 1427342015573 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 1427342015574 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 1427342015575 catalytic site [active] 1427342015576 subunit interface [polypeptide binding]; other site 1427342015577 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1427342015578 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1427342015579 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1427342015580 chaperone protein DnaJ; Provisional; Region: PRK10767 1427342015581 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 1427342015582 HSP70 interaction site [polypeptide binding]; other site 1427342015583 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1427342015584 substrate binding site [polypeptide binding]; other site 1427342015585 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1427342015586 Zn binding sites [ion binding]; other site 1427342015587 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1427342015588 dimer interface [polypeptide binding]; other site 1427342015589 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1427342015590 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1427342015591 nucleotide binding site [chemical binding]; other site 1427342015592 GrpE; Region: GrpE; pfam01025 1427342015593 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding; Region: GrpE; cd00446 1427342015594 dimer interface [polypeptide binding]; other site 1427342015595 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1427342015596 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1427342015597 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1427342015598 Walker A/P-loop; other site 1427342015599 ATP binding site [chemical binding]; other site 1427342015600 Q-loop/lid; other site 1427342015601 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1427342015602 ABC transporter signature motif; other site 1427342015603 Walker B; other site 1427342015604 D-loop; other site 1427342015605 H-loop/switch region; other site 1427342015606 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1427342015607 metal binding site 2 [ion binding]; metal-binding site 1427342015608 putative DNA binding helix; other site 1427342015609 metal binding site 1 [ion binding]; metal-binding site 1427342015610 dimer interface [polypeptide binding]; other site 1427342015611 structural Zn2+ binding site [ion binding]; other site 1427342015612 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1427342015613 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1427342015614 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 1427342015615 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1427342015616 putative coenzyme Q binding site [chemical binding]; other site 1427342015617 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 1427342015618 SmpB-tmRNA interface; other site 1427342015619 Transcriptional regulators [Transcription]; Region: FadR; COG2186 1427342015620 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342015621 DNA-binding site [nucleotide binding]; DNA binding site 1427342015622 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 1427342015623 glycolate transporter; Provisional; Region: PRK09695 1427342015624 L-lactate permease; Region: Lactate_perm; cl00701 1427342015625 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 1427342015626 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 1427342015627 phosphate binding site [ion binding]; other site 1427342015628 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1427342015629 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342015630 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 1427342015631 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1427342015632 S-adenosylmethionine decarboxylase proenzyme, Bacillus form; Region: SAM_DCase_Bsu; TIGR03330 1427342015633 spermidine synthase; Provisional; Region: PRK00811 1427342015634 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015635 S-adenosylmethionine binding site [chemical binding]; other site 1427342015636 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 1427342015637 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015638 active site 1427342015639 phosphorylation site [posttranslational modification] 1427342015640 intermolecular recognition site; other site 1427342015641 dimerization interface [polypeptide binding]; other site 1427342015642 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342015643 DNA binding site [nucleotide binding] 1427342015644 sensor protein QseC; Provisional; Region: PRK10337 1427342015645 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342015646 dimer interface [polypeptide binding]; other site 1427342015647 phosphorylation site [posttranslational modification] 1427342015648 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342015649 ATP binding site [chemical binding]; other site 1427342015650 Mg2+ binding site [ion binding]; other site 1427342015651 G-X-G motif; other site 1427342015652 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 1427342015653 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 1427342015654 DNA binding residues [nucleotide binding] 1427342015655 dimer interface [polypeptide binding]; other site 1427342015656 copper binding site [ion binding]; other site 1427342015657 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 1427342015658 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 1427342015659 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 1427342015660 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 1427342015661 ATP binding site [chemical binding]; other site 1427342015662 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 1427342015663 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015664 active site 1427342015665 phosphorylation site [posttranslational modification] 1427342015666 intermolecular recognition site; other site 1427342015667 dimerization interface [polypeptide binding]; other site 1427342015668 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342015669 Zn2+ binding site [ion binding]; other site 1427342015670 Mg2+ binding site [ion binding]; other site 1427342015671 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 1427342015672 EamA-like transporter family; Region: EamA; pfam00892 1427342015673 EamA-like transporter family; Region: EamA; pfam00892 1427342015674 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342015675 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342015676 putative DNA binding site [nucleotide binding]; other site 1427342015677 putative Zn2+ binding site [ion binding]; other site 1427342015678 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342015679 acetyl-CoA acetyltransferase; Provisional; Region: PRK09268 1427342015680 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1427342015681 dimer interface [polypeptide binding]; other site 1427342015682 active site 1427342015683 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08261 1427342015684 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342015685 NAD(P) binding site [chemical binding]; other site 1427342015686 active site 1427342015687 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342015688 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342015689 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342015690 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342015691 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342015692 active site 2 [active] 1427342015693 active site 1 [active] 1427342015694 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 1427342015695 homodimer interface [polypeptide binding]; other site 1427342015696 chemical substrate binding site [chemical binding]; other site 1427342015697 oligomer interface [polypeptide binding]; other site 1427342015698 metal binding site [ion binding]; metal-binding site 1427342015699 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015700 S-adenosylmethionine binding site [chemical binding]; other site 1427342015701 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 1427342015702 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 1427342015703 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial protein Rv2277c and similar proteins; Region: GDPD_Rv2277c_like; cd08580 1427342015704 putative active site [active] 1427342015705 catalytic site [active] 1427342015706 putative metal binding site [ion binding]; other site 1427342015707 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 1427342015708 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1427342015709 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342015710 Coenzyme A binding pocket [chemical binding]; other site 1427342015711 Predicted peroxiredoxins [General function prediction only]; Region: COG2044 1427342015712 glycine cleavage system protein H; Provisional; Region: PRK13380 1427342015713 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 1427342015714 lipoyl attachment site [posttranslational modification]; other site 1427342015715 Uncharacterized protein family (UPF0157); Region: UPF0157; pfam04229 1427342015716 Adenylate kinase and related kinases [Nucleotide transport and metabolism]; Region: Adk; COG0563 1427342015717 AAA domain; Region: AAA_17; pfam13207 1427342015718 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015719 S-adenosylmethionine binding site [chemical binding]; other site 1427342015720 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1427342015721 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 1427342015722 active site 1427342015723 catalytic triad [active] 1427342015724 dimer interface [polypeptide binding]; other site 1427342015725 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015726 S-adenosylmethionine binding site [chemical binding]; other site 1427342015727 Amino acid permease; Region: AA_permease; pfam00324 1427342015728 hypothetical protein; Provisional; Region: PRK07036 1427342015729 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342015730 inhibitor-cofactor binding pocket; inhibition site 1427342015731 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342015732 catalytic residue [active] 1427342015733 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1427342015734 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 1427342015735 DNA binding residues [nucleotide binding] 1427342015736 dimerization interface [polypeptide binding]; other site 1427342015737 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 1427342015738 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 1427342015739 G1 box; other site 1427342015740 putative GEF interaction site [polypeptide binding]; other site 1427342015741 GTP/Mg2+ binding site [chemical binding]; other site 1427342015742 Switch I region; other site 1427342015743 G2 box; other site 1427342015744 G3 box; other site 1427342015745 Switch II region; other site 1427342015746 G4 box; other site 1427342015747 G5 box; other site 1427342015748 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 1427342015749 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 1427342015750 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 1427342015751 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 1427342015752 selenocysteine synthase; Provisional; Region: PRK04311 1427342015753 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 1427342015754 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342015755 catalytic residue [active] 1427342015756 Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]; Region: FdhE; COG3058 1427342015757 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 1427342015758 Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]; Region: FdnI; COG2864 1427342015759 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 1427342015760 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 1427342015761 4Fe-4S binding domain; Region: Fer4; cl02805 1427342015762 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 1427342015763 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 1427342015764 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 1427342015765 [4Fe-4S] binding site [ion binding]; other site 1427342015766 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 1427342015767 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 1427342015768 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 1427342015769 molybdopterin cofactor binding site; other site 1427342015770 Lipase (class 2); Region: Lipase_2; pfam01674 1427342015771 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 1427342015772 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 1427342015773 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1427342015774 active site 1427342015775 FMN binding site [chemical binding]; other site 1427342015776 2,4-decadienoyl-CoA binding site; other site 1427342015777 catalytic residue [active] 1427342015778 4Fe-4S cluster binding site [ion binding]; other site 1427342015779 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 1427342015780 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342015781 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3238 1427342015782 Domain of unknown function (DUF1835); Region: DUF1835; pfam08874 1427342015783 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 1427342015784 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 1427342015785 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 1427342015786 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 1427342015787 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 1427342015788 Ligand binding site; other site 1427342015789 Putative Catalytic site; other site 1427342015790 DXD motif; other site 1427342015791 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 1427342015792 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 1427342015793 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 1427342015794 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1427342015795 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 1427342015796 PhoU domain; Region: PhoU; pfam01895 1427342015797 magnesium-transporting ATPase; Provisional; Region: PRK15122 1427342015798 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 1427342015799 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1427342015800 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 1427342015801 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1427342015802 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 1427342015803 Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NhoA; COG2162 1427342015804 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 1427342015805 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 1427342015806 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 1427342015807 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342015808 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1427342015809 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342015810 CoenzymeA binding site [chemical binding]; other site 1427342015811 subunit interaction site [polypeptide binding]; other site 1427342015812 PHB binding site; other site 1427342015813 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342015814 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342015815 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 1427342015816 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342015817 NAD(P) binding site [chemical binding]; other site 1427342015818 active site 1427342015819 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 1427342015820 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 1427342015821 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1427342015822 EamA-like transporter family; Region: EamA; pfam00892 1427342015823 EamA-like transporter family; Region: EamA; pfam00892 1427342015824 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4408 1427342015825 Uncharacterized protein conserved in bacteria (DUF2338); Region: DUF2338; pfam10100 1427342015826 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342015827 Nicotianamine synthase protein; Region: NAS; cl17658 1427342015828 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1427342015829 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 1427342015830 N-terminal plug; other site 1427342015831 ligand-binding site [chemical binding]; other site 1427342015832 Predicted membrane protein [Function unknown]; Region: COG3503 1427342015833 arginine decarboxylase; Provisional; Region: PRK05354 1427342015834 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 1427342015835 dimer interface [polypeptide binding]; other site 1427342015836 active site 1427342015837 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342015838 catalytic residues [active] 1427342015839 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1427342015840 translation initiation factor Sui1; Validated; Region: PRK06824 1427342015841 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 1427342015842 putative rRNA binding site [nucleotide binding]; other site 1427342015843 NUDIX hydrolase YfcD; Provisional; Region: PRK15393 1427342015844 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_38; cd04697 1427342015845 nudix motif; other site 1427342015846 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; pfam10095 1427342015847 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 1427342015848 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015849 active site 1427342015850 phosphorylation site [posttranslational modification] 1427342015851 intermolecular recognition site; other site 1427342015852 dimerization interface [polypeptide binding]; other site 1427342015853 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342015854 metal binding site [ion binding]; metal-binding site 1427342015855 active site 1427342015856 I-site; other site 1427342015857 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342015858 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342015859 dimer interface [polypeptide binding]; other site 1427342015860 putative CheW interface [polypeptide binding]; other site 1427342015861 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 1427342015862 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 1427342015863 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 1427342015864 DsbD alpha interface [polypeptide binding]; other site 1427342015865 catalytic residues [active] 1427342015866 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 1427342015867 Dehydroquinase class II; Region: DHquinase_II; pfam01220 1427342015868 active site 1427342015869 trimer interface [polypeptide binding]; other site 1427342015870 dimer interface [polypeptide binding]; other site 1427342015871 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 1427342015872 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342015873 carboxyltransferase (CT) interaction site; other site 1427342015874 biotinylation site [posttranslational modification]; other site 1427342015875 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 1427342015876 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342015877 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1427342015878 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1427342015879 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 1427342015880 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342015881 S-adenosylmethionine binding site [chemical binding]; other site 1427342015882 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1427342015883 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 1427342015884 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1427342015885 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 1427342015886 FMN binding site [chemical binding]; other site 1427342015887 active site 1427342015888 catalytic residues [active] 1427342015889 substrate binding site [chemical binding]; other site 1427342015890 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 1427342015891 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 1427342015892 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 1427342015893 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 1427342015894 purine monophosphate binding site [chemical binding]; other site 1427342015895 dimer interface [polypeptide binding]; other site 1427342015896 putative catalytic residues [active] 1427342015897 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 1427342015898 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 1427342015899 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 1427342015900 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 1427342015901 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 1427342015902 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 1427342015903 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 1427342015904 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 1427342015905 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342015906 dimer interface [polypeptide binding]; other site 1427342015907 phosphorylation site [posttranslational modification] 1427342015908 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342015909 ATP binding site [chemical binding]; other site 1427342015910 Mg2+ binding site [ion binding]; other site 1427342015911 G-X-G motif; other site 1427342015912 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342015913 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015914 active site 1427342015915 phosphorylation site [posttranslational modification] 1427342015916 intermolecular recognition site; other site 1427342015917 dimerization interface [polypeptide binding]; other site 1427342015918 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342015919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342015920 active site 1427342015921 phosphorylation site [posttranslational modification] 1427342015922 intermolecular recognition site; other site 1427342015923 dimerization interface [polypeptide binding]; other site 1427342015924 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 1427342015925 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 1427342015926 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 1427342015927 putative ligand binding site [chemical binding]; other site 1427342015928 HEAT repeats; Region: HEAT_2; pfam13646 1427342015929 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 1427342015930 TM-ABC transporter signature motif; other site 1427342015931 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 1427342015932 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342015933 TM-ABC transporter signature motif; other site 1427342015934 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 1427342015935 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 1427342015936 Walker A/P-loop; other site 1427342015937 ATP binding site [chemical binding]; other site 1427342015938 Q-loop/lid; other site 1427342015939 ABC transporter signature motif; other site 1427342015940 Walker B; other site 1427342015941 D-loop; other site 1427342015942 H-loop/switch region; other site 1427342015943 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 1427342015944 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 1427342015945 Walker A/P-loop; other site 1427342015946 ATP binding site [chemical binding]; other site 1427342015947 Q-loop/lid; other site 1427342015948 ABC transporter signature motif; other site 1427342015949 Walker B; other site 1427342015950 D-loop; other site 1427342015951 H-loop/switch region; other site 1427342015952 putative acetyltransferase; Provisional; Region: PRK03624 1427342015953 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342015954 Coenzyme A binding pocket [chemical binding]; other site 1427342015955 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 1427342015956 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 1427342015957 alpha-gamma subunit interface [polypeptide binding]; other site 1427342015958 beta-gamma subunit interface [polypeptide binding]; other site 1427342015959 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 1427342015960 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342015961 Coenzyme A binding pocket [chemical binding]; other site 1427342015962 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 1427342015963 gamma-beta subunit interface [polypeptide binding]; other site 1427342015964 alpha-beta subunit interface [polypeptide binding]; other site 1427342015965 urease subunit alpha; Reviewed; Region: ureC; PRK13207 1427342015966 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 1427342015967 subunit interactions [polypeptide binding]; other site 1427342015968 active site 1427342015969 flap region; other site 1427342015970 hypothetical protein; Provisional; Region: PRK11019 1427342015971 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 1427342015972 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 1427342015973 tetramer interface [polypeptide binding]; other site 1427342015974 active site 1427342015975 Mg2+/Mn2+ binding site [ion binding]; other site 1427342015976 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 1427342015977 putative chaperone; Provisional; Region: PRK11678 1427342015978 nucleotide binding site [chemical binding]; other site 1427342015979 putative NEF/HSP70 interaction site [polypeptide binding]; other site 1427342015980 SBD interface [polypeptide binding]; other site 1427342015981 psiF repeat; Region: PsiF_repeat; pfam07769 1427342015982 psiF repeat; Region: PsiF_repeat; pfam07769 1427342015983 psiF repeat; Region: PsiF_repeat; pfam07769 1427342015984 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 1427342015985 MOSC domain; Region: MOSC; pfam03473 1427342015986 DNA-binding transcriptional activator OsmE; Provisional; Region: PRK11251 1427342015987 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 1427342015988 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1427342015989 Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Region: HTH_BmrR; cd01107 1427342015990 DNA binding residues [nucleotide binding] 1427342015991 drug binding residues [chemical binding]; other site 1427342015992 dimer interface [polypeptide binding]; other site 1427342015993 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3708 1427342015994 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1427342015995 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1427342015996 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 1427342015997 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1427342015998 dinuclear metal binding motif [ion binding]; other site 1427342015999 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 1427342016000 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 1427342016001 Moco binding site; other site 1427342016002 metal coordination site [ion binding]; other site 1427342016003 Thiosulfate reductase cytochrome B subunit (membrane anchoring protein) [Energy production and conversion]; Region: COG4117 1427342016004 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 1427342016005 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 1427342016006 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342016007 active site 1427342016008 phosphorylation site [posttranslational modification] 1427342016009 intermolecular recognition site; other site 1427342016010 dimerization interface [polypeptide binding]; other site 1427342016011 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342016012 DNA binding site [nucleotide binding] 1427342016013 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 1427342016014 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342016015 dimerization interface [polypeptide binding]; other site 1427342016016 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342016017 dimer interface [polypeptide binding]; other site 1427342016018 phosphorylation site [posttranslational modification] 1427342016019 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342016020 ATP binding site [chemical binding]; other site 1427342016021 Mg2+ binding site [ion binding]; other site 1427342016022 G-X-G motif; other site 1427342016023 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342016024 putative MFS family transporter protein; Provisional; Region: PRK03633 1427342016025 putative substrate translocation pore; other site 1427342016026 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1427342016027 The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases...; Region: Delta6-FADS-like; cd03506 1427342016028 putative di-iron ligands [ion binding]; other site 1427342016029 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_2; cd06216 1427342016030 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 1427342016031 FAD binding pocket [chemical binding]; other site 1427342016032 FAD binding motif [chemical binding]; other site 1427342016033 phosphate binding motif [ion binding]; other site 1427342016034 beta-alpha-beta structure motif; other site 1427342016035 NAD binding pocket [chemical binding]; other site 1427342016036 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342016037 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1427342016038 catalytic loop [active] 1427342016039 iron binding site [ion binding]; other site 1427342016040 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 1427342016041 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342016042 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 1427342016043 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 1427342016044 dimer interface [polypeptide binding]; other site 1427342016045 catalytic residues [active] 1427342016046 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 1427342016047 UreF; Region: UreF; pfam01730 1427342016048 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 1427342016049 G1 box; other site 1427342016050 GTP/Mg2+ binding site [chemical binding]; other site 1427342016051 G2 box; other site 1427342016052 Switch I region; other site 1427342016053 G3 box; other site 1427342016054 Switch II region; other site 1427342016055 G4 box; other site 1427342016056 G5 box; other site 1427342016057 HupE / UreJ protein; Region: HupE_UreJ; cl01011 1427342016058 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 1427342016059 FecR protein; Region: FecR; pfam04773 1427342016060 RNA polymerase sigma factor; Provisional; Region: PRK12529 1427342016061 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1427342016062 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 1427342016063 DNA binding residues [nucleotide binding] 1427342016064 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342016065 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 1427342016066 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 1427342016067 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 1427342016068 outer membrane porin, OprD family; Region: OprD; pfam03573 1427342016069 NADP+-dependent p-hydroxybenzaldehyde dehydrogenase-like; Region: ALDH_HBenzADH; cd07151 1427342016070 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1427342016071 NAD(P) binding site [chemical binding]; other site 1427342016072 catalytic residues [active] 1427342016073 benzoate transport; Region: 2A0115; TIGR00895 1427342016074 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342016075 putative substrate translocation pore; other site 1427342016076 benzoylformate decarboxylase; Reviewed; Region: PRK07092 1427342016077 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342016078 PYR/PP interface [polypeptide binding]; other site 1427342016079 dimer interface [polypeptide binding]; other site 1427342016080 TPP binding site [chemical binding]; other site 1427342016081 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342016082 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 1427342016083 TPP-binding site [chemical binding]; other site 1427342016084 dimer interface [polypeptide binding]; other site 1427342016085 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342016086 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342016087 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 1427342016088 substrate binding pocket [chemical binding]; other site 1427342016089 dimerization interface [polypeptide binding]; other site 1427342016090 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342016091 putative substrate translocation pore; other site 1427342016092 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 1427342016093 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 1427342016094 iron-sulfur cluster [ion binding]; other site 1427342016095 [2Fe-2S] cluster binding site [ion binding]; other site 1427342016096 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 1427342016097 alpha subunit interface [polypeptide binding]; other site 1427342016098 active site 1427342016099 substrate binding site [chemical binding]; other site 1427342016100 Fe binding site [ion binding]; other site 1427342016101 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 1427342016102 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 1427342016103 FMN-binding pocket [chemical binding]; other site 1427342016104 flavin binding motif; other site 1427342016105 phosphate binding motif [ion binding]; other site 1427342016106 beta-alpha-beta structure motif; other site 1427342016107 NAD binding pocket [chemical binding]; other site 1427342016108 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342016109 catalytic loop [active] 1427342016110 iron binding site [ion binding]; other site 1427342016111 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342016112 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 1427342016113 DNA-binding site [nucleotide binding]; DNA binding site 1427342016114 FCD domain; Region: FCD; pfam07729 1427342016115 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 1427342016116 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 1427342016117 putative NAD(P) binding site [chemical binding]; other site 1427342016118 homodimer interface [polypeptide binding]; other site 1427342016119 homotetramer interface [polypeptide binding]; other site 1427342016120 active site 1427342016121 ornithine cyclodeaminase; Validated; Region: PRK06141 1427342016122 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 1427342016123 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 1427342016124 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 1427342016125 Walker A/P-loop; other site 1427342016126 ATP binding site [chemical binding]; other site 1427342016127 Q-loop/lid; other site 1427342016128 ABC transporter signature motif; other site 1427342016129 Walker B; other site 1427342016130 D-loop; other site 1427342016131 H-loop/switch region; other site 1427342016132 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 1427342016133 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 1427342016134 Walker A/P-loop; other site 1427342016135 ATP binding site [chemical binding]; other site 1427342016136 Q-loop/lid; other site 1427342016137 ABC transporter signature motif; other site 1427342016138 Walker B; other site 1427342016139 D-loop; other site 1427342016140 H-loop/switch region; other site 1427342016141 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 1427342016142 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 1427342016143 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 1427342016144 TM-ABC transporter signature motif; other site 1427342016145 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1427342016146 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 1427342016147 TM-ABC transporter signature motif; other site 1427342016148 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1427342016149 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 1427342016150 dimerization interface [polypeptide binding]; other site 1427342016151 ligand binding site [chemical binding]; other site 1427342016152 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342016153 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342016154 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342016155 dimerization interface [polypeptide binding]; other site 1427342016156 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1427342016157 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342016158 dimerization interface [polypeptide binding]; other site 1427342016159 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1427342016160 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342016161 dimer interface [polypeptide binding]; other site 1427342016162 putative CheW interface [polypeptide binding]; other site 1427342016163 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 1427342016164 nudix motif; other site 1427342016165 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 1427342016166 nicotinate (nicotinamide) nucleotide adenylyltransferase; Region: TIGR00482 1427342016167 active site 1427342016168 nucleotide binding site [chemical binding]; other site 1427342016169 HIGH motif; other site 1427342016170 KMSKS motif; other site 1427342016171 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 1427342016172 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342016173 catalytic triad [active] 1427342016174 metal binding site [ion binding]; metal-binding site 1427342016175 conserved cis-peptide bond; other site 1427342016176 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 1427342016177 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 1427342016178 active site 1427342016179 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 1427342016180 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 1427342016181 homodimer interface [polypeptide binding]; other site 1427342016182 NAD binding pocket [chemical binding]; other site 1427342016183 ATP binding pocket [chemical binding]; other site 1427342016184 Mg binding site [ion binding]; other site 1427342016185 active-site loop [active] 1427342016186 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 1427342016187 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 1427342016188 active site 1427342016189 catalytic triad [active] 1427342016190 oxyanion hole [active] 1427342016191 Azurin [Energy production and conversion]; Region: COG3241 1427342016192 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1427342016193 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342016194 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342016195 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1427342016196 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342016197 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1427342016198 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 1427342016199 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1427342016200 Uncharacterized conserved protein [Function unknown]; Region: COG2308 1427342016201 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 1427342016202 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 1427342016203 hypothetical protein; Provisional; Region: PRK01254 1427342016204 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 1427342016205 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 1427342016206 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 1427342016207 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 1427342016208 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342016209 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342016210 metal binding site [ion binding]; metal-binding site 1427342016211 active site 1427342016212 I-site; other site 1427342016213 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1427342016214 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 1427342016215 active site 1427342016216 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342016217 substrate binding site [chemical binding]; other site 1427342016218 catalytic residues [active] 1427342016219 dimer interface [polypeptide binding]; other site 1427342016220 replicative DNA helicase; Provisional; Region: PRK05748 1427342016221 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1427342016222 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 1427342016223 Walker A motif; other site 1427342016224 ATP binding site [chemical binding]; other site 1427342016225 Walker B motif; other site 1427342016226 DNA binding loops [nucleotide binding] 1427342016227 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1427342016228 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1427342016229 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1427342016230 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1427342016231 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1427342016232 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 1427342016233 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 1427342016234 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1427342016235 exoribonuclease R; Provisional; Region: PRK11642 1427342016236 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 1427342016237 RNB domain; Region: RNB; pfam00773 1427342016238 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 1427342016239 RNA binding site [nucleotide binding]; other site 1427342016240 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 1427342016241 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 1427342016242 GDP-binding site [chemical binding]; other site 1427342016243 ACT binding site; other site 1427342016244 IMP binding site; other site 1427342016245 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 1427342016246 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 1427342016247 dimer interface [polypeptide binding]; other site 1427342016248 motif 1; other site 1427342016249 active site 1427342016250 motif 2; other site 1427342016251 motif 3; other site 1427342016252 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3242 1427342016253 FtsH protease regulator HflC; Provisional; Region: PRK11029 1427342016254 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 1427342016255 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 1427342016256 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 1427342016257 HflK protein; Region: hflK; TIGR01933 1427342016258 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 1427342016259 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 1427342016260 HflX GTPase family; Region: HflX; cd01878 1427342016261 G1 box; other site 1427342016262 GTP/Mg2+ binding site [chemical binding]; other site 1427342016263 Switch I region; other site 1427342016264 G2 box; other site 1427342016265 G3 box; other site 1427342016266 Switch II region; other site 1427342016267 G4 box; other site 1427342016268 G5 box; other site 1427342016269 bacterial Hfq-like; Region: Hfq; cd01716 1427342016270 hexamer interface [polypeptide binding]; other site 1427342016271 Sm1 motif; other site 1427342016272 RNA binding site [nucleotide binding]; other site 1427342016273 Sm2 motif; other site 1427342016274 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1427342016275 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1427342016276 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1427342016277 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342016278 ATP binding site [chemical binding]; other site 1427342016279 Mg2+ binding site [ion binding]; other site 1427342016280 G-X-G motif; other site 1427342016281 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 1427342016282 ATP binding site [chemical binding]; other site 1427342016283 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1427342016284 AMIN domain; Region: AMIN; pfam11741 1427342016285 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1427342016286 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 1427342016287 active site 1427342016288 metal binding site [ion binding]; metal-binding site 1427342016289 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 1427342016290 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342016291 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 1427342016292 putative carbohydrate kinase; Provisional; Region: PRK10565 1427342016293 Uncharacterized conserved protein [Function unknown]; Region: COG0062 1427342016294 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 1427342016295 putative substrate binding site [chemical binding]; other site 1427342016296 putative ATP binding site [chemical binding]; other site 1427342016297 epoxyqueuosine reductase; Region: TIGR00276 1427342016298 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 1427342016299 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 1427342016300 catalytic site [active] 1427342016301 putative active site [active] 1427342016302 putative substrate binding site [chemical binding]; other site 1427342016303 dimer interface [polypeptide binding]; other site 1427342016304 GTPase RsgA; Reviewed; Region: PRK12288 1427342016305 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1427342016306 RNA binding site [nucleotide binding]; other site 1427342016307 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 1427342016308 GTPase/Zn-binding domain interface [polypeptide binding]; other site 1427342016309 GTP/Mg2+ binding site [chemical binding]; other site 1427342016310 G4 box; other site 1427342016311 G5 box; other site 1427342016312 G1 box; other site 1427342016313 Switch I region; other site 1427342016314 G2 box; other site 1427342016315 G3 box; other site 1427342016316 Switch II region; other site 1427342016317 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 1427342016318 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 1427342016319 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1427342016320 ligand binding site [chemical binding]; other site 1427342016321 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 1427342016322 flagellar motor protein MotA; Validated; Region: PRK09110 1427342016323 HDOD domain; Region: HDOD; pfam08668 1427342016324 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 1427342016325 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 1427342016326 active site residue [active] 1427342016327 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 1427342016328 active site residue [active] 1427342016329 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 1427342016330 Src homology 2 (SH2) domain; Region: SH2; cl15255 1427342016331 phosphotyrosine binding pocket [polypeptide binding]; other site 1427342016332 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1427342016333 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 1427342016334 active site 1427342016335 phosphorylation site [posttranslational modification] 1427342016336 dimerization interface [polypeptide binding]; other site 1427342016337 PAS fold; Region: PAS; pfam00989 1427342016338 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342016339 putative active site [active] 1427342016340 heme pocket [chemical binding]; other site 1427342016341 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342016342 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342016343 metal binding site [ion binding]; metal-binding site 1427342016344 active site 1427342016345 I-site; other site 1427342016346 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342016347 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 1427342016348 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 1427342016349 phosphoserine phosphatase SerB; Region: serB; TIGR00338 1427342016350 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342016351 motif II; other site 1427342016352 Uncharacterized membrane protein affecting hemolysin expression [General function prediction only]; Region: AhpA; COG3726 1427342016353 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 1427342016354 metal binding site [ion binding]; metal-binding site 1427342016355 Predicted membrane-bound metal-dependent hydrolases [General function prediction only]; Region: COG1988 1427342016356 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 1427342016357 Protein of unknown function (DUF330); Region: DUF330; pfam03886 1427342016358 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1427342016359 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 1427342016360 CAP-like domain; other site 1427342016361 active site 1427342016362 primary dimer interface [polypeptide binding]; other site 1427342016363 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1427342016364 catalytic motif [active] 1427342016365 Catalytic residue [active] 1427342016366 SdiA-regulated; Region: SdiA-regulated; cd09971 1427342016367 putative active site [active] 1427342016368 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 1427342016369 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342016370 ATP binding site [chemical binding]; other site 1427342016371 Mg2+ binding site [ion binding]; other site 1427342016372 G-X-G motif; other site 1427342016373 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 1427342016374 anchoring element; other site 1427342016375 dimer interface [polypeptide binding]; other site 1427342016376 ATP binding site [chemical binding]; other site 1427342016377 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 1427342016378 active site 1427342016379 metal binding site [ion binding]; metal-binding site 1427342016380 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1427342016381 Predicted esterase [General function prediction only]; Region: COG3150 1427342016382 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1427342016383 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 1427342016384 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1427342016385 active site 1427342016386 metal binding site [ion binding]; metal-binding site 1427342016387 hexamer interface [polypeptide binding]; other site 1427342016388 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3151 1427342016389 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 1427342016390 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 1427342016391 dimer interface [polypeptide binding]; other site 1427342016392 ADP-ribose binding site [chemical binding]; other site 1427342016393 active site 1427342016394 nudix motif; other site 1427342016395 metal binding site [ion binding]; metal-binding site 1427342016396 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 1427342016397 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 1427342016398 ThiC-associated domain; Region: ThiC-associated; pfam13667 1427342016399 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 1427342016400 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 1427342016401 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1427342016402 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1427342016403 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 1427342016404 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342016405 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342016406 homodimer interface [polypeptide binding]; other site 1427342016407 catalytic residue [active] 1427342016408 hypothetical protein; Provisional; Region: PRK07524 1427342016409 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1427342016410 PYR/PP interface [polypeptide binding]; other site 1427342016411 dimer interface [polypeptide binding]; other site 1427342016412 TPP binding site [chemical binding]; other site 1427342016413 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342016414 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 1427342016415 TPP-binding site [chemical binding]; other site 1427342016416 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 1427342016417 CoA binding domain; Region: CoA_binding_2; pfam13380 1427342016418 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 1427342016419 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 1427342016420 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342016421 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342016422 active site 1427342016423 enoyl-CoA hydratase; Provisional; Region: PRK06688 1427342016424 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1427342016425 substrate binding site [chemical binding]; other site 1427342016426 oxyanion hole (OAH) forming residues; other site 1427342016427 trimer interface [polypeptide binding]; other site 1427342016428 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 1427342016429 S-methylmethionine transporter; Provisional; Region: PRK11387 1427342016430 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1427342016431 HAMP domain; Region: HAMP; pfam00672 1427342016432 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342016433 dimer interface [polypeptide binding]; other site 1427342016434 phosphorylation site [posttranslational modification] 1427342016435 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342016436 ATP binding site [chemical binding]; other site 1427342016437 Mg2+ binding site [ion binding]; other site 1427342016438 G-X-G motif; other site 1427342016439 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342016440 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342016441 active site 1427342016442 phosphorylation site [posttranslational modification] 1427342016443 intermolecular recognition site; other site 1427342016444 dimerization interface [polypeptide binding]; other site 1427342016445 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342016446 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016447 substrate binding pocket [chemical binding]; other site 1427342016448 membrane-bound complex binding site; other site 1427342016449 hinge residues; other site 1427342016450 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 1427342016451 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342016452 active site 1427342016453 phosphorylation site [posttranslational modification] 1427342016454 intermolecular recognition site; other site 1427342016455 dimerization interface [polypeptide binding]; other site 1427342016456 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342016457 DNA binding site [nucleotide binding] 1427342016458 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 1427342016459 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342016460 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 1427342016461 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 1427342016462 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1427342016463 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 1427342016464 Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_3_FMN; cd04734 1427342016465 putative active site [active] 1427342016466 putative FMN binding site [chemical binding]; other site 1427342016467 putative substrate binding site [chemical binding]; other site 1427342016468 putative catalytic residue [active] 1427342016469 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 1427342016470 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342016471 non-specific DNA binding site [nucleotide binding]; other site 1427342016472 salt bridge; other site 1427342016473 sequence-specific DNA binding site [nucleotide binding]; other site 1427342016474 Cupin domain; Region: Cupin_2; pfam07883 1427342016475 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1427342016476 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1427342016477 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1427342016478 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342016479 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342016480 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342016481 dimerization interface [polypeptide binding]; other site 1427342016482 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 1427342016483 FAD dependent oxidoreductase; Region: DAO; pfam01266 1427342016484 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342016485 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1427342016486 active site 1427342016487 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1427342016488 catalytic tetrad [active] 1427342016489 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342016490 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342016491 active site 1427342016492 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1427342016493 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342016494 active site 1427342016495 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 1427342016496 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 1427342016497 putative ribose interaction site [chemical binding]; other site 1427342016498 putative ADP binding site [chemical binding]; other site 1427342016499 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 1427342016500 active site 1427342016501 nucleotide binding site [chemical binding]; other site 1427342016502 HIGH motif; other site 1427342016503 KMSKS motif; other site 1427342016504 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 1427342016505 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1427342016506 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 1427342016507 Walker A/P-loop; other site 1427342016508 ATP binding site [chemical binding]; other site 1427342016509 Q-loop/lid; other site 1427342016510 ABC transporter signature motif; other site 1427342016511 Walker B; other site 1427342016512 D-loop; other site 1427342016513 H-loop/switch region; other site 1427342016514 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1427342016515 active site 1427342016516 substrate binding site [chemical binding]; other site 1427342016517 ATP binding site [chemical binding]; other site 1427342016518 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1427342016519 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 1427342016520 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342016521 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 1427342016522 active site 1427342016523 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 1427342016524 Mig-14; Region: Mig-14; pfam07395 1427342016525 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 1427342016526 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 1427342016527 putative ADP-binding pocket [chemical binding]; other site 1427342016528 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342016529 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 1427342016530 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 1427342016531 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 1427342016532 active site 1427342016533 ATP binding site [chemical binding]; other site 1427342016534 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 1427342016535 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 1427342016536 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 1427342016537 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 1427342016538 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342016539 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 1427342016540 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1427342016541 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 1427342016542 putative active site [active] 1427342016543 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 1427342016544 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 1427342016545 putative active site [active] 1427342016546 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1427342016547 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 1427342016548 homodimer interface [polypeptide binding]; other site 1427342016549 substrate-cofactor binding pocket; other site 1427342016550 catalytic residue [active] 1427342016551 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 1427342016552 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 1427342016553 metal binding triad; other site 1427342016554 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 1427342016555 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 1427342016556 metal binding triad; other site 1427342016557 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 1427342016558 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 1427342016559 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 1427342016560 dimer interface [polypeptide binding]; other site 1427342016561 TPP-binding site [chemical binding]; other site 1427342016562 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1427342016563 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_long; TIGR01348 1427342016564 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342016565 E3 interaction surface; other site 1427342016566 lipoyl attachment site [posttranslational modification]; other site 1427342016567 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342016568 E3 interaction surface; other site 1427342016569 lipoyl attachment site [posttranslational modification]; other site 1427342016570 e3 binding domain; Region: E3_binding; pfam02817 1427342016571 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1427342016572 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 1427342016573 GAF domain; Region: GAF; pfam01590 1427342016574 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342016575 PAS domain; Region: PAS_9; pfam13426 1427342016576 putative active site [active] 1427342016577 heme pocket [chemical binding]; other site 1427342016578 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342016579 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342016580 metal binding site [ion binding]; metal-binding site 1427342016581 active site 1427342016582 I-site; other site 1427342016583 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342016584 methionine sulfoxide reductase A; Provisional; Region: PRK00058 1427342016585 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 1427342016586 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342016587 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342016588 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342016589 active site 1427342016590 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342016591 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain [Inorganic ion transport and metabolism]; Region: COG3263 1427342016592 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1427342016593 TrkA-C domain; Region: TrkA_C; pfam02080 1427342016594 Transporter associated domain; Region: CorC_HlyC; smart01091 1427342016595 hypothetical protein; Provisional; Region: PRK11281 1427342016596 Vegetative insecticide protein 3A N terminal; Region: Vip3A_N; pfam12495 1427342016597 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 1427342016598 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342016599 Uncharacterized conserved protein [Function unknown]; Region: COG0397 1427342016600 hypothetical protein; Validated; Region: PRK00029 1427342016601 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1427342016602 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 1427342016603 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 1427342016604 homodimer interface [polypeptide binding]; other site 1427342016605 substrate-cofactor binding pocket; other site 1427342016606 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342016607 catalytic residue [active] 1427342016608 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342016609 CoenzymeA binding site [chemical binding]; other site 1427342016610 subunit interaction site [polypeptide binding]; other site 1427342016611 PHB binding site; other site 1427342016612 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342016613 Ligand Binding Site [chemical binding]; other site 1427342016614 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1427342016615 Ligand Binding Site [chemical binding]; other site 1427342016616 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1427342016617 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342016618 P-loop; other site 1427342016619 Magnesium ion binding site [ion binding]; other site 1427342016620 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342016621 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 1427342016622 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342016623 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342016624 dimerization interface [polypeptide binding]; other site 1427342016625 substrate binding pocket [chemical binding]; other site 1427342016626 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342016627 putative substrate translocation pore; other site 1427342016628 short chain dehydrogenase; Provisional; Region: PRK06197 1427342016629 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342016630 NAD(P) binding site [chemical binding]; other site 1427342016631 active site 1427342016632 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342016633 Helix-turn-helix domain; Region: HTH_18; pfam12833 1427342016634 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342016635 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1427342016636 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 1427342016637 substrate binding site [chemical binding]; other site 1427342016638 active site 1427342016639 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 1427342016640 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342016641 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342016642 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 1427342016643 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 1427342016644 active site 1427342016645 dimer interface [polypeptide binding]; other site 1427342016646 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 1427342016647 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 1427342016648 active site 1427342016649 FMN binding site [chemical binding]; other site 1427342016650 substrate binding site [chemical binding]; other site 1427342016651 3Fe-4S cluster binding site [ion binding]; other site 1427342016652 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 1427342016653 domain interface; other site 1427342016654 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 1427342016655 AAA ATPase domain; Region: AAA_16; pfam13191 1427342016656 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 1427342016657 Sporulation related domain; Region: SPOR; pfam05036 1427342016658 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 1427342016659 active site 1427342016660 dimer interface [polypeptide binding]; other site 1427342016661 metal binding site [ion binding]; metal-binding site 1427342016662 shikimate kinase; Reviewed; Region: aroK; PRK00131 1427342016663 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 1427342016664 ADP binding site [chemical binding]; other site 1427342016665 magnesium binding site [ion binding]; other site 1427342016666 putative shikimate binding site; other site 1427342016667 AMIN domain; Region: AMIN; pfam11741 1427342016668 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 1427342016669 Secretin and TonB N terminus short domain; Region: STN; smart00965 1427342016670 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1427342016671 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1427342016672 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 1427342016673 Pilus assembly protein, PilP; Region: PilP; pfam04351 1427342016674 Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilO; COG3167 1427342016675 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 1427342016676 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 1427342016677 Competence protein A; Region: Competence_A; pfam11104 1427342016678 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1427342016679 nucleotide binding site [chemical binding]; other site 1427342016680 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1427342016681 Transglycosylase; Region: Transgly; pfam00912 1427342016682 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1427342016683 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 1427342016684 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1427342016685 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1427342016686 putative NAD(P) binding site [chemical binding]; other site 1427342016687 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 1427342016688 Peptidase family M48; Region: Peptidase_M48; pfam01435 1427342016689 Staphylococcal nuclease homologues; Region: SNc; smart00318 1427342016690 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 1427342016691 Catalytic site; other site 1427342016692 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 1427342016693 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 1427342016694 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342016695 ATP binding site [chemical binding]; other site 1427342016696 putative Mg++ binding site [ion binding]; other site 1427342016697 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1427342016698 nucleotide binding region [chemical binding]; other site 1427342016699 ATP-binding site [chemical binding]; other site 1427342016700 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1427342016701 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 1427342016702 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1427342016703 active site 1427342016704 HIGH motif; other site 1427342016705 KMSK motif region; other site 1427342016706 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1427342016707 tRNA binding surface [nucleotide binding]; other site 1427342016708 anticodon binding site; other site 1427342016709 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 1427342016710 Sporulation related domain; Region: SPOR; pfam05036 1427342016711 ATP-dependent protease subunit HslV; Provisional; Region: PRK05456 1427342016712 active site 1427342016713 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1427342016714 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342016715 Walker A motif; other site 1427342016716 ATP binding site [chemical binding]; other site 1427342016717 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1427342016718 Walker B motif; other site 1427342016719 arginine finger; other site 1427342016720 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1427342016721 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 1427342016722 poly(R)-hydroxyalkanoic acid synthase, class II; Region: PHA_synth_II; TIGR01839 1427342016723 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 1427342016724 poly(3-hydroxyalkanoate) depolymerase; Region: PHA_depoly_arom; TIGR02240 1427342016725 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1427342016726 poly(R)-hydroxyalkanoic acid synthase, class II; Region: PHA_synth_II; TIGR01839 1427342016727 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 1427342016728 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1427342016729 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342016730 Bacterial transcriptional repressor; Region: TetR; pfam13972 1427342016731 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 1427342016732 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 1427342016733 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 1427342016734 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1427342016735 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342016736 S-adenosylmethionine binding site [chemical binding]; other site 1427342016737 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 1427342016738 SCP-2 sterol transfer family; Region: SCP2; pfam02036 1427342016739 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 1427342016740 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1427342016741 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 1427342016742 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 1427342016743 metal binding site [ion binding]; metal-binding site 1427342016744 twin arginine translocase protein A; Provisional; Region: tatA; PRK00442 1427342016745 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1427342016746 sec-independent translocase; Provisional; Region: tatB; PRK00404 1427342016747 twin arginine-targeting protein translocase TatB; Region: tatB; TIGR01410 1427342016748 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 1427342016749 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 1427342016750 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1427342016751 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1427342016752 dimer interface [polypeptide binding]; other site 1427342016753 putative CheW interface [polypeptide binding]; other site 1427342016754 Uncharacterized protein family (UPF0158); Region: UPF0158; pfam03682 1427342016755 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342016756 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342016757 Walker A/P-loop; other site 1427342016758 ATP binding site [chemical binding]; other site 1427342016759 Q-loop/lid; other site 1427342016760 ABC transporter signature motif; other site 1427342016761 Walker B; other site 1427342016762 D-loop; other site 1427342016763 H-loop/switch region; other site 1427342016764 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342016765 dimer interface [polypeptide binding]; other site 1427342016766 conserved gate region; other site 1427342016767 putative PBP binding loops; other site 1427342016768 ABC-ATPase subunit interface; other site 1427342016769 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342016770 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016771 substrate binding pocket [chemical binding]; other site 1427342016772 membrane-bound complex binding site; other site 1427342016773 hinge residues; other site 1427342016774 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1427342016775 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 1427342016776 Ligand binding site; other site 1427342016777 DXD motif; other site 1427342016778 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 1427342016779 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; pfam04349 1427342016780 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 1427342016781 putative active site [active] 1427342016782 dimerization interface [polypeptide binding]; other site 1427342016783 putative tRNAtyr binding site [nucleotide binding]; other site 1427342016784 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 1427342016785 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1427342016786 TAP-like protein; Region: Abhydrolase_4; pfam08386 1427342016787 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 1427342016788 nudix motif; other site 1427342016789 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342016790 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016791 substrate binding pocket [chemical binding]; other site 1427342016792 membrane-bound complex binding site; other site 1427342016793 hinge residues; other site 1427342016794 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 1427342016795 homotrimer interaction site [polypeptide binding]; other site 1427342016796 putative active site [active] 1427342016797 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 1427342016798 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1427342016799 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 1427342016800 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342016801 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342016802 dimerization interface [polypeptide binding]; other site 1427342016803 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1427342016804 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 1427342016805 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1427342016806 putative active site [active] 1427342016807 catalytic site [active] 1427342016808 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1427342016809 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1427342016810 putative active site [active] 1427342016811 catalytic site [active] 1427342016812 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342016813 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342016814 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342016815 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 1427342016816 N-formylglutamate amidohydrolase; Region: FGase; cl01522 1427342016817 imidazolonepropionase; Validated; Region: PRK09356 1427342016818 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 1427342016819 active site 1427342016820 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 1427342016821 active sites [active] 1427342016822 tetramer interface [polypeptide binding]; other site 1427342016823 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1427342016824 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 1427342016825 Walker A/P-loop; other site 1427342016826 ATP binding site [chemical binding]; other site 1427342016827 Q-loop/lid; other site 1427342016828 ABC transporter signature motif; other site 1427342016829 Walker B; other site 1427342016830 D-loop; other site 1427342016831 H-loop/switch region; other site 1427342016832 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342016833 dimer interface [polypeptide binding]; other site 1427342016834 conserved gate region; other site 1427342016835 putative PBP binding loops; other site 1427342016836 ABC-ATPase subunit interface; other site 1427342016837 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342016838 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 1427342016839 putative proline-specific permease; Provisional; Region: proY; PRK10580 1427342016840 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 1427342016841 active sites [active] 1427342016842 tetramer interface [polypeptide binding]; other site 1427342016843 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 1427342016844 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 1427342016845 Na binding site [ion binding]; other site 1427342016846 urocanate hydratase; Provisional; Region: PRK05414 1427342016847 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 1427342016848 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 1427342016849 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 1427342016850 putative di-iron ligands [ion binding]; other site 1427342016851 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342016852 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 1427342016853 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3758 1427342016854 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 1427342016855 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342016856 DNA-binding site [nucleotide binding]; DNA binding site 1427342016857 UTRA domain; Region: UTRA; pfam07702 1427342016858 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 1427342016859 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_E; cd01313 1427342016860 active site 1427342016861 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 1427342016862 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 1427342016863 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 1427342016864 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3803 1427342016865 fructose-1,6-bisphosphatase family protein; Region: PLN02628 1427342016866 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 1427342016867 AMP binding site [chemical binding]; other site 1427342016868 metal binding site [ion binding]; metal-binding site 1427342016869 active site 1427342016870 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 1427342016871 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1427342016872 dimer interface [polypeptide binding]; other site 1427342016873 active site 1427342016874 metal binding site [ion binding]; metal-binding site 1427342016875 glutathione binding site [chemical binding]; other site 1427342016876 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 1427342016877 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: Triacylglycerol_lipase_like; cd01847 1427342016878 active site 1427342016879 catalytic triad [active] 1427342016880 oxyanion hole [active] 1427342016881 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1427342016882 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 1427342016883 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 1427342016884 Predicted membrane protein [Function unknown]; Region: COG5373 1427342016885 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342016886 S-adenosylmethionine binding site [chemical binding]; other site 1427342016887 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 1427342016888 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 1427342016889 DNA binding residues [nucleotide binding] 1427342016890 putative dimer interface [polypeptide binding]; other site 1427342016891 putative metal binding residues [ion binding]; other site 1427342016892 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1427342016893 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1427342016894 G1 box; other site 1427342016895 putative GEF interaction site [polypeptide binding]; other site 1427342016896 GTP/Mg2+ binding site [chemical binding]; other site 1427342016897 Switch I region; other site 1427342016898 G2 box; other site 1427342016899 G3 box; other site 1427342016900 Switch II region; other site 1427342016901 G4 box; other site 1427342016902 G5 box; other site 1427342016903 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 1427342016904 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 1427342016905 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 1427342016906 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 1427342016907 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 1427342016908 Ligand Binding Site [chemical binding]; other site 1427342016909 thiazole biosynthesis domain; Region: ThiI_C_thiazole; TIGR04271 1427342016910 glutamine synthetase; Provisional; Region: glnA; PRK09469 1427342016911 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 1427342016912 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342016913 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1427342016914 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342016915 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 1427342016916 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 1427342016917 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 1427342016918 PAS domain; Region: PAS; smart00091 1427342016919 putative active site [active] 1427342016920 heme pocket [chemical binding]; other site 1427342016921 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342016922 dimer interface [polypeptide binding]; other site 1427342016923 phosphorylation site [posttranslational modification] 1427342016924 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342016925 ATP binding site [chemical binding]; other site 1427342016926 Mg2+ binding site [ion binding]; other site 1427342016927 G-X-G motif; other site 1427342016928 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 1427342016929 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342016930 active site 1427342016931 phosphorylation site [posttranslational modification] 1427342016932 intermolecular recognition site; other site 1427342016933 dimerization interface [polypeptide binding]; other site 1427342016934 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342016935 Walker A motif; other site 1427342016936 ATP binding site [chemical binding]; other site 1427342016937 Walker B motif; other site 1427342016938 arginine finger; other site 1427342016939 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342016940 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 1427342016941 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 1427342016942 SecA binding site; other site 1427342016943 Preprotein binding site; other site 1427342016944 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 1427342016945 GSH binding site [chemical binding]; other site 1427342016946 catalytic residues [active] 1427342016947 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 1427342016948 active site residue [active] 1427342016949 phosphoglyceromutase; Provisional; Region: PRK05434 1427342016950 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 1427342016951 CAAX protease self-immunity; Region: Abi; pfam02517 1427342016952 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 1427342016953 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342016954 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1427342016955 C-terminal peptidase (prc); Region: prc; TIGR00225 1427342016956 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 1427342016957 protein binding site [polypeptide binding]; other site 1427342016958 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1427342016959 Catalytic dyad [active] 1427342016960 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 1427342016961 NodB motif; other site 1427342016962 putative active site [active] 1427342016963 putative catalytic site [active] 1427342016964 Zn binding site [ion binding]; other site 1427342016965 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342016966 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016967 substrate binding pocket [chemical binding]; other site 1427342016968 membrane-bound complex binding site; other site 1427342016969 hinge residues; other site 1427342016970 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016971 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342016972 substrate binding pocket [chemical binding]; other site 1427342016973 membrane-bound complex binding site; other site 1427342016974 hinge residues; other site 1427342016975 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342016976 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342016977 substrate binding pocket [chemical binding]; other site 1427342016978 membrane-bound complex binding site; other site 1427342016979 hinge residues; other site 1427342016980 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 1427342016981 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 1427342016982 substrate binding site [chemical binding]; other site 1427342016983 glutamase interaction surface [polypeptide binding]; other site 1427342016984 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 1427342016985 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 1427342016986 catalytic residues [active] 1427342016987 Uncharacterized conserved protein (DUF2164); Region: DUF2164; pfam09932 1427342016988 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 1427342016989 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 1427342016990 putative active site [active] 1427342016991 oxyanion strand; other site 1427342016992 catalytic triad [active] 1427342016993 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 1427342016994 putative active site pocket [active] 1427342016995 4-fold oligomerization interface [polypeptide binding]; other site 1427342016996 metal binding residues [ion binding]; metal-binding site 1427342016997 3-fold/trimer interface [polypeptide binding]; other site 1427342016998 Acetyltransferase (GNAT) domain; Region: DUF3749; pfam12568 1427342016999 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cl00477 1427342017000 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1427342017001 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1427342017002 AsmA family; Region: AsmA; pfam05170 1427342017003 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1427342017004 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1427342017005 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 1427342017006 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1427342017007 minor groove reading motif; other site 1427342017008 helix-hairpin-helix signature motif; other site 1427342017009 substrate binding pocket [chemical binding]; other site 1427342017010 active site 1427342017011 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 1427342017012 DNA binding and oxoG recognition site [nucleotide binding] 1427342017013 oxidative damage protection protein; Provisional; Region: PRK05408 1427342017014 putative oxidoreductase; Provisional; Region: PRK11579 1427342017015 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1427342017016 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1427342017017 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342017018 classical (c) SDRs; Region: SDR_c; cd05233 1427342017019 NAD(P) binding site [chemical binding]; other site 1427342017020 active site 1427342017021 Uncharacterized conserved protein [Function unknown]; Region: COG2928 1427342017022 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 1427342017023 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1427342017024 Walker A/P-loop; other site 1427342017025 ATP binding site [chemical binding]; other site 1427342017026 Q-loop/lid; other site 1427342017027 ABC transporter signature motif; other site 1427342017028 Walker B; other site 1427342017029 D-loop; other site 1427342017030 H-loop/switch region; other site 1427342017031 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1427342017032 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342017033 substrate binding pocket [chemical binding]; other site 1427342017034 membrane-bound complex binding site; other site 1427342017035 hinge residues; other site 1427342017036 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342017037 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017038 dimer interface [polypeptide binding]; other site 1427342017039 conserved gate region; other site 1427342017040 putative PBP binding loops; other site 1427342017041 ABC-ATPase subunit interface; other site 1427342017042 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1427342017043 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017044 dimer interface [polypeptide binding]; other site 1427342017045 conserved gate region; other site 1427342017046 putative PBP binding loops; other site 1427342017047 ABC-ATPase subunit interface; other site 1427342017048 Methyltransferase domain; Region: Methyltransf_32; pfam13679 1427342017049 MarR family; Region: MarR_2; cl17246 1427342017050 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1427342017051 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 1427342017052 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 1427342017053 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1427342017054 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342017055 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1427342017056 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017057 putative substrate translocation pore; other site 1427342017058 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017059 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 1427342017060 HTH-like domain; Region: HTH_21; pfam13276 1427342017061 Integrase core domain; Region: rve; pfam00665 1427342017062 Integrase core domain; Region: rve_3; pfam13683 1427342017063 Transposase; Region: HTH_Tnp_1; pfam01527 1427342017064 portal vertex protein; Provisional; Region: Q; PHA02536 1427342017065 Phage portal protein; Region: Phage_portal; pfam04860 1427342017066 terminase ATPase subunit; Provisional; Region: P; PHA02535 1427342017067 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 1427342017068 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 1427342017069 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; pfam05929 1427342017070 Phage major capsid protein, P2 family; Region: Phage_cap_P2; pfam05125 1427342017071 terminase endonuclease subunit; Provisional; Region: M; PHA02537 1427342017072 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 1427342017073 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 1427342017074 Phage Tail Protein X; Region: Phage_tail_X; pfam05489 1427342017075 Protein of unknown function (DUF754); Region: DUF754; pfam05449 1427342017076 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1427342017077 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 1427342017078 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 1427342017079 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 1427342017080 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 1427342017081 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 1427342017082 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 1427342017083 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 1427342017084 baseplate wedge subunit; Provisional; Region: W; PHA02516 1427342017085 baseplate assembly protein; Provisional; Region: J; PHA02568 1427342017086 phage tail protein, P2 protein I family; Region: tail_P2_I; TIGR01634 1427342017087 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 1427342017088 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 1427342017089 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 1427342017090 major tail sheath protein; Provisional; Region: FI; PHA02560 1427342017091 major tail tube protein; Provisional; Region: FII; PHA02600 1427342017092 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 1427342017093 Phage P2 GpE; Region: Phage_P2_GpE; pfam06528 1427342017094 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 1427342017095 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 1427342017096 tail protein; Provisional; Region: D; PHA02561 1427342017097 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 1427342017098 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 1427342017099 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 1427342017100 active site 1427342017101 metal binding site [ion binding]; metal-binding site 1427342017102 interdomain interaction site; other site 1427342017103 DksA-like zinc finger domain containing protein; Region: PHA00080 1427342017104 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1427342017105 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 1427342017106 substrate interaction site [chemical binding]; other site 1427342017107 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 1427342017108 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342017109 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342017110 active site 1427342017111 DNA binding site [nucleotide binding] 1427342017112 Int/Topo IB signature motif; other site 1427342017113 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 1427342017114 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 1427342017115 NAD binding site [chemical binding]; other site 1427342017116 substrate binding site [chemical binding]; other site 1427342017117 homodimer interface [polypeptide binding]; other site 1427342017118 active site 1427342017119 dTDP-4-dehydrorhamnose reductase; Region: rmlD; TIGR01214 1427342017120 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1427342017121 NADP binding site [chemical binding]; other site 1427342017122 active site 1427342017123 putative substrate binding site [chemical binding]; other site 1427342017124 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 1427342017125 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 1427342017126 substrate binding site; other site 1427342017127 tetramer interface; other site 1427342017128 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 1427342017129 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 1427342017130 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342017131 dimer interface [polypeptide binding]; other site 1427342017132 phosphorylation site [posttranslational modification] 1427342017133 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342017134 ATP binding site [chemical binding]; other site 1427342017135 Mg2+ binding site [ion binding]; other site 1427342017136 G-X-G motif; other site 1427342017137 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342017138 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342017139 active site 1427342017140 phosphorylation site [posttranslational modification] 1427342017141 intermolecular recognition site; other site 1427342017142 dimerization interface [polypeptide binding]; other site 1427342017143 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342017144 Walker A motif; other site 1427342017145 ATP binding site [chemical binding]; other site 1427342017146 Walker B motif; other site 1427342017147 arginine finger; other site 1427342017148 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342017149 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 1427342017150 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 1427342017151 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 1427342017152 DctM-like transporters; Region: DctM; pfam06808 1427342017153 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 1427342017154 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 1427342017155 arginine deiminase; Provisional; Region: PRK01388 1427342017156 ornithine carbamoyltransferase; Validated; Region: PRK02102 1427342017157 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1427342017158 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1427342017159 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 1427342017160 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 1427342017161 putative substrate binding site [chemical binding]; other site 1427342017162 nucleotide binding site [chemical binding]; other site 1427342017163 nucleotide binding site [chemical binding]; other site 1427342017164 homodimer interface [polypeptide binding]; other site 1427342017165 "elongating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type I and II and polyketide synthases.They are characterized by the utlization of acyl carrier protein (ACP)...; Region: elong_cond_enzymes; cd00828 1427342017166 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 1427342017167 active site 1427342017168 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1427342017169 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 1427342017170 active site 1427342017171 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 1427342017172 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 1427342017173 dimer interface [polypeptide binding]; other site 1427342017174 ADP-ribose binding site [chemical binding]; other site 1427342017175 active site 1427342017176 nudix motif; other site 1427342017177 metal binding site [ion binding]; metal-binding site 1427342017178 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 1427342017179 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342017180 motif II; other site 1427342017181 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 1427342017182 BON domain; Region: BON; pfam04972 1427342017183 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1427342017184 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342017185 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017186 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342017187 dimerization interface [polypeptide binding]; other site 1427342017188 Uncharacterized protein required for formate dehydrogenase activity [Energy production and conversion]; Region: FdhD; COG1526 1427342017189 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 1427342017190 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 1427342017191 putative molybdopterin cofactor binding site [chemical binding]; other site 1427342017192 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 1427342017193 putative molybdopterin cofactor binding site; other site 1427342017194 Global regulator protein family; Region: CsrA; pfam02599 1427342017195 chorismate mutase; Provisional; Region: PRK09269 1427342017196 chorismate mutase, putative; Region: CM_mono2; TIGR01806 1427342017197 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342017198 active site 1427342017199 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1427342017200 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 1427342017201 putative active site [active] 1427342017202 metal binding site [ion binding]; metal-binding site 1427342017203 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 1427342017204 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 1427342017205 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1427342017206 active site 1427342017207 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 1427342017208 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1427342017209 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342017210 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342017211 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342017212 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1427342017213 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017214 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 1427342017215 dimerization interface [polypeptide binding]; other site 1427342017216 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 1427342017217 dimer interface [polypeptide binding]; other site 1427342017218 FMN binding site [chemical binding]; other site 1427342017219 Fimbrial protein; Region: Fimbrial; cl01416 1427342017220 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 1427342017221 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 1427342017222 active site 1427342017223 substrate-binding site [chemical binding]; other site 1427342017224 metal-binding site [ion binding] 1427342017225 ATP binding site [chemical binding]; other site 1427342017226 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 1427342017227 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 1427342017228 dimerization interface [polypeptide binding]; other site 1427342017229 domain crossover interface; other site 1427342017230 redox-dependent activation switch; other site 1427342017231 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1427342017232 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 1427342017233 active site 1427342017234 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 1427342017235 RNA binding surface [nucleotide binding]; other site 1427342017236 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 1427342017237 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 1427342017238 RimK-like ATP-grasp domain; Region: RimK; pfam08443 1427342017239 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1427342017240 dimer interface [polypeptide binding]; other site 1427342017241 catalytic triad [active] 1427342017242 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 1427342017243 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342017244 dimerization interface [polypeptide binding]; other site 1427342017245 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342017246 ATP binding site [chemical binding]; other site 1427342017247 Mg2+ binding site [ion binding]; other site 1427342017248 G-X-G motif; other site 1427342017249 osmolarity response regulator; Provisional; Region: ompR; PRK09468 1427342017250 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342017251 active site 1427342017252 phosphorylation site [posttranslational modification] 1427342017253 intermolecular recognition site; other site 1427342017254 dimerization interface [polypeptide binding]; other site 1427342017255 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342017256 DNA binding site [nucleotide binding] 1427342017257 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 1427342017258 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 1427342017259 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 1427342017260 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 1427342017261 RNA binding site [nucleotide binding]; other site 1427342017262 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342017263 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 1427342017264 CoenzymeA binding site [chemical binding]; other site 1427342017265 subunit interaction site [polypeptide binding]; other site 1427342017266 PHB binding site; other site 1427342017267 glutamate--cysteine ligase; Provisional; Region: PRK02107 1427342017268 N-acetylglutamate synthase; Validated; Region: PRK05279 1427342017269 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 1427342017270 putative feedback inhibition sensing region; other site 1427342017271 putative nucleotide binding site [chemical binding]; other site 1427342017272 putative substrate binding site [chemical binding]; other site 1427342017273 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1427342017274 Coenzyme A binding pocket [chemical binding]; other site 1427342017275 inner membrane protein; Provisional; Region: PRK10995 1427342017276 acetylornithine deacetylase; Provisional; Region: PRK05111 1427342017277 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 1427342017278 metal binding site [ion binding]; metal-binding site 1427342017279 putative dimer interface [polypeptide binding]; other site 1427342017280 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342017281 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1427342017282 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 1427342017283 Uncharacterized conserved protein [Function unknown]; Region: COG3025 1427342017284 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 1427342017285 putative active site [active] 1427342017286 putative metal binding residues [ion binding]; other site 1427342017287 signature motif; other site 1427342017288 putative triphosphate binding site [ion binding]; other site 1427342017289 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 1427342017290 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 1427342017291 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 1427342017292 Walker A motif; other site 1427342017293 ATP binding site [chemical binding]; other site 1427342017294 Walker B motif; other site 1427342017295 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1427342017296 Protein of unknown function (DUF2388); Region: DUF2388; pfam09498 1427342017297 glycine dehydrogenase; Provisional; Region: PRK12566 1427342017298 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1427342017299 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1427342017300 catalytic residue [active] 1427342017301 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 1427342017302 tetramer interface [polypeptide binding]; other site 1427342017303 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342017304 catalytic residue [active] 1427342017305 glycine cleavage system protein H; Provisional; Region: PRK13380 1427342017306 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 1427342017307 lipoyl attachment site [posttranslational modification]; other site 1427342017308 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 1427342017309 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1427342017310 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 1427342017311 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017312 dimer interface [polypeptide binding]; other site 1427342017313 conserved gate region; other site 1427342017314 putative PBP binding loops; other site 1427342017315 ABC-ATPase subunit interface; other site 1427342017316 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1427342017317 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1427342017318 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 1427342017319 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017320 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 1427342017321 dimerization interface [polypeptide binding]; other site 1427342017322 substrate binding pocket [chemical binding]; other site 1427342017323 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342017324 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017325 putative substrate translocation pore; other site 1427342017326 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK05714 1427342017327 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1427342017328 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1427342017329 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK05732 1427342017330 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 1427342017331 hypothetical protein; Reviewed; Region: PRK02166 1427342017332 TIGR02449 family protein; Region: TIGR02449 1427342017333 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1427342017334 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1427342017335 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1427342017336 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 1427342017337 Uncharacterized conserved protein [Function unknown]; Region: COG2947 1427342017338 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1427342017339 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1427342017340 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 1427342017341 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1427342017342 Walker A/P-loop; other site 1427342017343 ATP binding site [chemical binding]; other site 1427342017344 Q-loop/lid; other site 1427342017345 ABC transporter signature motif; other site 1427342017346 Walker B; other site 1427342017347 D-loop; other site 1427342017348 H-loop/switch region; other site 1427342017349 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1427342017350 Walker A/P-loop; other site 1427342017351 ATP binding site [chemical binding]; other site 1427342017352 Q-loop/lid; other site 1427342017353 ABC transporter signature motif; other site 1427342017354 Walker B; other site 1427342017355 D-loop; other site 1427342017356 H-loop/switch region; other site 1427342017357 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1427342017358 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 1427342017359 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 1427342017360 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1427342017361 HlyD family secretion protein; Region: HlyD_3; pfam13437 1427342017362 flagellar basal body-associated protein FliL-like protein; Validated; Region: PRK05697 1427342017363 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 1427342017364 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 1427342017365 NAD(P) binding site [chemical binding]; other site 1427342017366 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 1427342017367 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017368 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017369 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 1427342017370 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342017371 catalytic loop [active] 1427342017372 iron binding site [ion binding]; other site 1427342017373 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 1427342017374 FAD binding pocket [chemical binding]; other site 1427342017375 FAD binding motif [chemical binding]; other site 1427342017376 phosphate binding motif [ion binding]; other site 1427342017377 beta-alpha-beta structure motif; other site 1427342017378 NAD binding pocket [chemical binding]; other site 1427342017379 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1427342017380 Acyltransferase family; Region: Acyl_transf_3; pfam01757 1427342017381 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1427342017382 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 1427342017383 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 1427342017384 RNA binding site [nucleotide binding]; other site 1427342017385 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 1427342017386 multimer interface [polypeptide binding]; other site 1427342017387 Walker A motif; other site 1427342017388 ATP binding site [chemical binding]; other site 1427342017389 Walker B motif; other site 1427342017390 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 1427342017391 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1427342017392 catalytic residues [active] 1427342017393 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1427342017394 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1427342017395 polyphosphate kinase; Provisional; Region: PRK05443 1427342017396 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 1427342017397 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 1427342017398 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 1427342017399 putative domain interface [polypeptide binding]; other site 1427342017400 putative active site [active] 1427342017401 catalytic site [active] 1427342017402 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 1427342017403 putative domain interface [polypeptide binding]; other site 1427342017404 putative active site [active] 1427342017405 catalytic site [active] 1427342017406 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 1427342017407 dimer interface [polypeptide binding]; other site 1427342017408 active site 1427342017409 aspartate-rich active site metal binding site; other site 1427342017410 allosteric magnesium binding site [ion binding]; other site 1427342017411 Schiff base residues; other site 1427342017412 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1427342017413 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1427342017414 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 1427342017415 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 1427342017416 conserved cys residue [active] 1427342017417 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 1427342017418 CoenzymeA binding site [chemical binding]; other site 1427342017419 subunit interaction site [polypeptide binding]; other site 1427342017420 PHB binding site; other site 1427342017421 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1671 1427342017422 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1427342017423 Cytochrome c; Region: Cytochrom_C; pfam00034 1427342017424 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 1427342017425 LysE type translocator; Region: LysE; cl00565 1427342017426 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 1427342017427 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1427342017428 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1427342017429 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 1427342017430 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342017431 Walker A/P-loop; other site 1427342017432 ATP binding site [chemical binding]; other site 1427342017433 Q-loop/lid; other site 1427342017434 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342017435 ABC transporter; Region: ABC_tran_2; pfam12848 1427342017436 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1427342017437 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 1427342017438 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1427342017439 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 1427342017440 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1427342017441 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 1427342017442 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 1427342017443 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 1427342017444 HemY protein N-terminus; Region: HemY_N; pfam07219 1427342017445 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1427342017446 binding surface 1427342017447 TPR motif; other site 1427342017448 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 1427342017449 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 1427342017450 uroporphyrinogen-III synthase; Validated; Region: PRK05752 1427342017451 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 1427342017452 active site 1427342017453 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1427342017454 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 1427342017455 domain interfaces; other site 1427342017456 active site 1427342017457 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 1427342017458 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342017459 active site 1427342017460 phosphorylation site [posttranslational modification] 1427342017461 intermolecular recognition site; other site 1427342017462 dimerization interface [polypeptide binding]; other site 1427342017463 LytTr DNA-binding domain; Region: LytTR; pfam04397 1427342017464 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 1427342017465 Histidine kinase; Region: His_kinase; pfam06580 1427342017466 argininosuccinate lyase; Provisional; Region: PRK00855 1427342017467 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 1427342017468 active sites [active] 1427342017469 tetramer interface [polypeptide binding]; other site 1427342017470 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 1427342017471 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 1427342017472 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 1427342017473 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 1427342017474 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 1427342017475 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1427342017476 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1427342017477 Cl binding site [ion binding]; other site 1427342017478 oligomer interface [polypeptide binding]; other site 1427342017479 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 1427342017480 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342017481 substrate binding pocket [chemical binding]; other site 1427342017482 membrane-bound complex binding site; other site 1427342017483 hinge residues; other site 1427342017484 TIGR02647 family protein; Region: DNA 1427342017485 Adenylate cyclase [Nucleotide transport and metabolism]; Region: CyaA; COG3072 1427342017486 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 1427342017487 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 1427342017488 Uncharacterized conserved protein [Function unknown]; Region: COG4278 1427342017489 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 1427342017490 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1427342017491 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 1427342017492 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 1427342017493 putative iron binding site [ion binding]; other site 1427342017494 Predicted small periplasmic lipoprotein [Cell motility and secretion]; Region: COG5567 1427342017495 diaminopimelate decarboxylase; Region: lysA; TIGR01048 1427342017496 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 1427342017497 active site 1427342017498 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342017499 substrate binding site [chemical binding]; other site 1427342017500 catalytic residues [active] 1427342017501 dimer interface [polypeptide binding]; other site 1427342017502 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 1427342017503 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1427342017504 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1427342017505 Protein of unknown function, DUF484; Region: DUF484; pfam04340 1427342017506 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 1427342017507 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 1427342017508 active site 1427342017509 DNA binding site [nucleotide binding] 1427342017510 Int/Topo IB signature motif; other site 1427342017511 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 1427342017512 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 1427342017513 motif II; other site 1427342017514 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342017515 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342017516 DNA-binding site [nucleotide binding]; DNA binding site 1427342017517 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342017518 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342017519 homodimer interface [polypeptide binding]; other site 1427342017520 catalytic residue [active] 1427342017521 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 1427342017522 Uncharacterized conserved protein [Function unknown]; Region: COG0432 1427342017523 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 1427342017524 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 1427342017525 Nitrogen regulatory protein P-II; Region: P-II; smart00938 1427342017526 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2960 1427342017527 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1427342017528 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1427342017529 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1427342017530 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1427342017531 BCCT family transporter; Region: BCCT; cl00569 1427342017532 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1427342017533 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 1427342017534 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017535 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 1427342017536 dimerization interface [polypeptide binding]; other site 1427342017537 substrate binding pocket [chemical binding]; other site 1427342017538 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342017539 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342017540 metal binding site [ion binding]; metal-binding site 1427342017541 active site 1427342017542 I-site; other site 1427342017543 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342017544 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 1427342017545 Part of AAA domain; Region: AAA_19; pfam13245 1427342017546 Family description; Region: UvrD_C_2; pfam13538 1427342017547 pyruvate dehydrogenase; Provisional; Region: PRK09124 1427342017548 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 1427342017549 PYR/PP interface [polypeptide binding]; other site 1427342017550 dimer interface [polypeptide binding]; other site 1427342017551 tetramer interface [polypeptide binding]; other site 1427342017552 TPP binding site [chemical binding]; other site 1427342017553 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1427342017554 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 1427342017555 TPP-binding site [chemical binding]; other site 1427342017556 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342017557 active site 1427342017558 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 1427342017559 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 1427342017560 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 1427342017561 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 1427342017562 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342017563 non-specific DNA binding site [nucleotide binding]; other site 1427342017564 salt bridge; other site 1427342017565 sequence-specific DNA binding site [nucleotide binding]; other site 1427342017566 Cupin domain; Region: Cupin_2; pfam07883 1427342017567 alanine racemase; Reviewed; Region: dadX; PRK03646 1427342017568 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 1427342017569 active site 1427342017570 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342017571 substrate binding site [chemical binding]; other site 1427342017572 catalytic residues [active] 1427342017573 dimer interface [polypeptide binding]; other site 1427342017574 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 1427342017575 homotrimer interaction site [polypeptide binding]; other site 1427342017576 putative active site [active] 1427342017577 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 1427342017578 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342017579 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 1427342017580 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 1427342017581 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 1427342017582 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1427342017583 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 1427342017584 putative DNA binding site [nucleotide binding]; other site 1427342017585 putative Zn2+ binding site [ion binding]; other site 1427342017586 AsnC family; Region: AsnC_trans_reg; pfam01037 1427342017587 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342017588 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1427342017589 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 1427342017590 PLD-like domain; Region: PLDc_2; pfam13091 1427342017591 putative active site [active] 1427342017592 catalytic site [active] 1427342017593 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 1427342017594 PLD-like domain; Region: PLDc_2; pfam13091 1427342017595 putative active site [active] 1427342017596 catalytic site [active] 1427342017597 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017598 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1427342017599 putative substrate translocation pore; other site 1427342017600 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 1427342017601 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 1427342017602 NAD(P) binding site [chemical binding]; other site 1427342017603 catalytic residues [active] 1427342017604 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 1427342017605 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342017606 inhibitor-cofactor binding pocket; inhibition site 1427342017607 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342017608 catalytic residue [active] 1427342017609 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 1427342017610 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 1427342017611 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 1427342017612 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1427342017613 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1427342017614 peptide binding site [polypeptide binding]; other site 1427342017615 hypothetical protein; Reviewed; Region: PRK00024 1427342017616 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1427342017617 MPN+ (JAMM) motif; other site 1427342017618 Zinc-binding site [ion binding]; other site 1427342017619 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 1427342017620 Flavoprotein; Region: Flavoprotein; pfam02441 1427342017621 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 1427342017622 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1427342017623 trimer interface [polypeptide binding]; other site 1427342017624 active site 1427342017625 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1427342017626 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 1427342017627 active site 1427342017628 substrate binding site [chemical binding]; other site 1427342017629 metal binding site [ion binding]; metal-binding site 1427342017630 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 1427342017631 feedback inhibition sensing region; other site 1427342017632 homohexameric interface [polypeptide binding]; other site 1427342017633 nucleotide binding site [chemical binding]; other site 1427342017634 N-acetyl-L-glutamate binding site [chemical binding]; other site 1427342017635 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 1427342017636 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1427342017637 SurA N-terminal domain; Region: SurA_N; pfam09312 1427342017638 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342017639 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 1427342017640 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 1427342017641 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3; Region: PLPDE_III_DSD_D-TA_like_3; cd06814 1427342017642 dimer interface [polypeptide binding]; other site 1427342017643 active site 1427342017644 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1427342017645 substrate binding site [chemical binding]; other site 1427342017646 catalytic residue [active] 1427342017647 FAD-linked oxidoreductase; Region: bact_FAD_ox; TIGR01679 1427342017648 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342017649 D-arabinono-1,4-lactone oxidase; Region: ALO; pfam04030 1427342017650 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 1427342017651 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342017652 active site 1427342017653 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1427342017654 active site 1427342017655 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 1427342017656 putative active site [active] 1427342017657 putative catalytic site [active] 1427342017658 putative DNA binding site [nucleotide binding]; other site 1427342017659 putative phosphate binding site [ion binding]; other site 1427342017660 metal binding site A [ion binding]; metal-binding site 1427342017661 putative AP binding site [nucleotide binding]; other site 1427342017662 putative metal binding site B [ion binding]; other site 1427342017663 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 1427342017664 ribonuclease PH; Reviewed; Region: rph; PRK00173 1427342017665 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1427342017666 hexamer interface [polypeptide binding]; other site 1427342017667 active site 1427342017668 hypothetical protein; Provisional; Region: PRK11820 1427342017669 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 1427342017670 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 1427342017671 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1427342017672 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 1427342017673 catalytic site [active] 1427342017674 G-X2-G-X-G-K; other site 1427342017675 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 1427342017676 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 1427342017677 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1427342017678 Zn2+ binding site [ion binding]; other site 1427342017679 Mg2+ binding site [ion binding]; other site 1427342017680 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1427342017681 synthetase active site [active] 1427342017682 NTP binding site [chemical binding]; other site 1427342017683 metal binding site [ion binding]; metal-binding site 1427342017684 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 1427342017685 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 1427342017686 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 1427342017687 homotrimer interaction site [polypeptide binding]; other site 1427342017688 putative active site [active] 1427342017689 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1427342017690 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1427342017691 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1427342017692 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342017693 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1427342017694 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 1427342017695 putative NAD(P) binding site [chemical binding]; other site 1427342017696 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 1427342017697 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017698 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 1427342017699 dimerization interface [polypeptide binding]; other site 1427342017700 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 1427342017701 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 1427342017702 ssDNA binding site; other site 1427342017703 generic binding surface II; other site 1427342017704 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 1427342017705 ATP binding site [chemical binding]; other site 1427342017706 putative Mg++ binding site [ion binding]; other site 1427342017707 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 1427342017708 nucleotide binding region [chemical binding]; other site 1427342017709 ATP-binding site [chemical binding]; other site 1427342017710 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 1427342017711 putative deacylase active site [active] 1427342017712 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 1427342017713 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 1427342017714 IHF dimer interface [polypeptide binding]; other site 1427342017715 IHF - DNA interface [nucleotide binding]; other site 1427342017716 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 1427342017717 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1427342017718 Rubredoxin [Energy production and conversion]; Region: COG1773 1427342017719 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 1427342017720 iron binding site [ion binding]; other site 1427342017721 Rubredoxin [Energy production and conversion]; Region: COG1773 1427342017722 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 1427342017723 iron binding site [ion binding]; other site 1427342017724 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 1427342017725 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 1427342017726 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 1427342017727 Cysteine-rich domain; Region: CCG; pfam02754 1427342017728 Cysteine-rich domain; Region: CCG; pfam02754 1427342017729 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342017730 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 1427342017731 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 1427342017732 FAD binding domain; Region: FAD_binding_4; pfam01565 1427342017733 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 1427342017734 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342017735 DNA-binding site [nucleotide binding]; DNA binding site 1427342017736 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 1427342017737 Chorismate lyase; Region: Chor_lyase; pfam04345 1427342017738 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 1427342017739 UbiA prenyltransferase family; Region: UbiA; pfam01040 1427342017740 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 1427342017741 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 1427342017742 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 1427342017743 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342017744 active site 1427342017745 phosphorylation site [posttranslational modification] 1427342017746 intermolecular recognition site; other site 1427342017747 dimerization interface [polypeptide binding]; other site 1427342017748 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 1427342017749 DNA binding site [nucleotide binding] 1427342017750 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 1427342017751 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1427342017752 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342017753 putative active site [active] 1427342017754 heme pocket [chemical binding]; other site 1427342017755 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342017756 dimer interface [polypeptide binding]; other site 1427342017757 phosphorylation site [posttranslational modification] 1427342017758 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342017759 ATP binding site [chemical binding]; other site 1427342017760 Mg2+ binding site [ion binding]; other site 1427342017761 G-X-G motif; other site 1427342017762 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1427342017763 Domain of unknown function DUF21; Region: DUF21; pfam01595 1427342017764 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 1427342017765 Transporter associated domain; Region: CorC_HlyC; smart01091 1427342017766 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 1427342017767 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1427342017768 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342017769 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342017770 Response regulator receiver domain; Region: Response_reg; pfam00072 1427342017771 active site 1427342017772 phosphorylation site [posttranslational modification] 1427342017773 intermolecular recognition site; other site 1427342017774 dimerization interface [polypeptide binding]; other site 1427342017775 transcriptional regulator PhoU; Provisional; Region: PRK11115 1427342017776 PhoU domain; Region: PhoU; pfam01895 1427342017777 PhoU domain; Region: PhoU; pfam01895 1427342017778 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 1427342017779 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 1427342017780 Walker A/P-loop; other site 1427342017781 ATP binding site [chemical binding]; other site 1427342017782 Q-loop/lid; other site 1427342017783 ABC transporter signature motif; other site 1427342017784 Walker B; other site 1427342017785 D-loop; other site 1427342017786 H-loop/switch region; other site 1427342017787 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 1427342017788 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 1427342017789 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017790 dimer interface [polypeptide binding]; other site 1427342017791 conserved gate region; other site 1427342017792 putative PBP binding loops; other site 1427342017793 ABC-ATPase subunit interface; other site 1427342017794 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 1427342017795 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017796 ABC-ATPase subunit interface; other site 1427342017797 PBP superfamily domain; Region: PBP_like_2; cl17296 1427342017798 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342017799 metabolite-proton symporter; Region: 2A0106; TIGR00883 1427342017800 putative substrate translocation pore; other site 1427342017801 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 1427342017802 choline dehydrogenase; Validated; Region: PRK02106 1427342017803 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1427342017804 betaine aldehyde dehydrogenase; Provisional; Region: PRK13252 1427342017805 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 1427342017806 tetrameric interface [polypeptide binding]; other site 1427342017807 NAD binding site [chemical binding]; other site 1427342017808 catalytic residues [active] 1427342017809 transcriptional regulator BetI; Validated; Region: PRK00767 1427342017810 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1427342017811 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 1427342017812 Choline-glycine betaine transporter [Cell envelope biogenesis, outer membrane]; Region: BetT; COG1292 1427342017813 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 1427342017814 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1427342017815 Walker A/P-loop; other site 1427342017816 ATP binding site [chemical binding]; other site 1427342017817 Q-loop/lid; other site 1427342017818 ABC transporter signature motif; other site 1427342017819 Walker B; other site 1427342017820 D-loop; other site 1427342017821 H-loop/switch region; other site 1427342017822 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342017823 dimer interface [polypeptide binding]; other site 1427342017824 conserved gate region; other site 1427342017825 putative PBP binding loops; other site 1427342017826 ABC-ATPase subunit interface; other site 1427342017827 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342017828 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 1427342017829 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 1427342017830 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 1427342017831 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 1427342017832 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 1427342017833 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 1427342017834 conserved cys residue [active] 1427342017835 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1427342017836 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 1427342017837 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017838 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 1427342017839 putative dimerization interface [polypeptide binding]; other site 1427342017840 Conserved hypothetical protein 698; Region: Cons_hypoth698; pfam03601 1427342017841 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 1427342017842 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 1427342017843 active site 1427342017844 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07066 1427342017845 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1427342017846 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1427342017847 Uncharacterized conserved protein [Function unknown]; Region: COG3246 1427342017848 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 1427342017849 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 1427342017850 acetylornithine deacetylase; Provisional; Region: PRK07522 1427342017851 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 1427342017852 metal binding site [ion binding]; metal-binding site 1427342017853 putative dimer interface [polypeptide binding]; other site 1427342017854 Uncharacterized conserved protein [Function unknown]; Region: COG3342 1427342017855 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 1427342017856 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 1427342017857 homotrimer interaction site [polypeptide binding]; other site 1427342017858 putative active site [active] 1427342017859 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342017860 flavin-dependent oxidoreductase, MSMEG_0569 family; Region: MSMEG_0569_nitr; TIGR04046 1427342017861 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 1427342017862 Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Region: PLDc_PaCLS_like_1; cd09155 1427342017863 putative active site [active] 1427342017864 catalytic site [active] 1427342017865 Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Region: PLDc_PaCLS_like_2; cd09161 1427342017866 putative active site [active] 1427342017867 catalytic site [active] 1427342017868 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 1427342017869 SnoaL-like domain; Region: SnoaL_2; pfam12680 1427342017870 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 1427342017871 Membrane dipeptidase (Peptidase family M19); Region: Peptidase_M19; pfam01244 1427342017872 active site 1427342017873 V4R domain; Region: V4R; cl15268 1427342017874 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 1427342017875 Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_3_FMN; cd04734 1427342017876 putative active site [active] 1427342017877 putative FMN binding site [chemical binding]; other site 1427342017878 putative substrate binding site [chemical binding]; other site 1427342017879 putative catalytic residue [active] 1427342017880 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1427342017881 Domain of unknown function (DUF3483); Region: DUF3483; pfam11982 1427342017882 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1427342017883 Cysteine-rich domain; Region: CCG; pfam02754 1427342017884 Cysteine-rich domain; Region: CCG; pfam02754 1427342017885 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 1427342017886 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1427342017887 Ligand Binding Site [chemical binding]; other site 1427342017888 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1427342017889 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 1427342017890 Ligand Binding Site [chemical binding]; other site 1427342017891 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1427342017892 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 1427342017893 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1427342017894 non-specific DNA binding site [nucleotide binding]; other site 1427342017895 salt bridge; other site 1427342017896 sequence-specific DNA binding site [nucleotide binding]; other site 1427342017897 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 1427342017898 Cell division protein ZapA; Region: ZapA; pfam05164 1427342017899 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 1427342017900 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 1427342017901 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 1427342017902 [2Fe-2S] cluster binding site [ion binding]; other site 1427342017903 C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_GbcA-like; cd08884 1427342017904 putative alpha subunit interface [polypeptide binding]; other site 1427342017905 putative active site [active] 1427342017906 putative substrate binding site [chemical binding]; other site 1427342017907 Fe binding site [ion binding]; other site 1427342017908 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 1427342017909 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 1427342017910 FAD binding pocket [chemical binding]; other site 1427342017911 FAD binding motif [chemical binding]; other site 1427342017912 phosphate binding motif [ion binding]; other site 1427342017913 beta-alpha-beta structure motif; other site 1427342017914 NAD binding pocket [chemical binding]; other site 1427342017915 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 1427342017916 catalytic loop [active] 1427342017917 iron binding site [ion binding]; other site 1427342017918 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 1427342017919 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 1427342017920 tetramer interface [polypeptide binding]; other site 1427342017921 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342017922 catalytic residue [active] 1427342017923 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1427342017924 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 1427342017925 dimer interface [polypeptide binding]; other site 1427342017926 active site 1427342017927 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1427342017928 folate binding site [chemical binding]; other site 1427342017929 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 1427342017930 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1427342017931 Sarcosine oxidase delta subunit [Amino acid transport and metabolism]; Region: SoxD; COG4311 1427342017932 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 1427342017933 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 1427342017934 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1427342017935 Sarcosine oxidase gamma subunit [Amino acid transport and metabolism]; Region: COG4583 1427342017936 formyltetrahydrofolate deformylase; Reviewed; Region: PRK13011 1427342017937 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 1427342017938 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 1427342017939 putative active site [active] 1427342017940 putative substrate binding site [chemical binding]; other site 1427342017941 putative cosubstrate binding site; other site 1427342017942 catalytic site [active] 1427342017943 formaldehyde dehydrogenase, glutathione-independent; Region: fdhA_non_GSH; TIGR02819 1427342017944 Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH); Region: PFDH_like; cd08282 1427342017945 NAD binding site [chemical binding]; other site 1427342017946 catalytic Zn binding site [ion binding]; other site 1427342017947 structural Zn binding site [ion binding]; other site 1427342017948 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 1427342017949 active site 1427342017950 phosphate binding residues; other site 1427342017951 catalytic residues [active] 1427342017952 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3495 1427342017953 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 1427342017954 ATP-grasp domain; Region: ATP-grasp; pfam02222 1427342017955 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 1427342017956 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1427342017957 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 1427342017958 NAD binding site [chemical binding]; other site 1427342017959 substrate binding site [chemical binding]; other site 1427342017960 catalytic Zn binding site [ion binding]; other site 1427342017961 tetramer interface [polypeptide binding]; other site 1427342017962 structural Zn binding site [ion binding]; other site 1427342017963 cell density-dependent motility repressor; Provisional; Region: PRK10082 1427342017964 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342017965 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1427342017966 dimerization interface [polypeptide binding]; other site 1427342017967 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 1427342017968 Aspartase; Region: Aspartase; cd01357 1427342017969 active sites [active] 1427342017970 tetramer interface [polypeptide binding]; other site 1427342017971 Sulphur transport; Region: Sulf_transp; pfam04143 1427342017972 Predicted transporter component [General function prediction only]; Region: COG2391 1427342017973 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1427342017974 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342017975 DNA-binding site [nucleotide binding]; DNA binding site 1427342017976 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 1427342017977 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342017978 homodimer interface [polypeptide binding]; other site 1427342017979 catalytic residue [active] 1427342017980 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342017981 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1427342017982 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342017983 tryptophan permease; Provisional; Region: PRK10483 1427342017984 aromatic amino acid transport protein; Region: araaP; TIGR00837 1427342017985 pyruvate carboxylase subunit B; Validated; Region: PRK09282 1427342017986 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 1427342017987 active site 1427342017988 catalytic residues [active] 1427342017989 metal binding site [ion binding]; metal-binding site 1427342017990 homodimer binding site [polypeptide binding]; other site 1427342017991 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 1427342017992 carboxyltransferase (CT) interaction site; other site 1427342017993 biotinylation site [posttranslational modification]; other site 1427342017994 pyruvate carboxylase subunit A; Validated; Region: PRK07178 1427342017995 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1427342017996 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1427342017997 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1427342017998 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 1427342017999 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1427342018000 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 1427342018001 putative dimerization interface [polypeptide binding]; other site 1427342018002 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 1427342018003 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 1427342018004 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 1427342018005 putative active site [active] 1427342018006 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 1427342018007 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1427342018008 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1427342018009 putative protease; Provisional; Region: PRK15452 1427342018010 Peptidase family U32; Region: Peptidase_U32; pfam01136 1427342018011 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 1427342018012 PAS fold; Region: PAS_3; pfam08447 1427342018013 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342018014 heme pocket [chemical binding]; other site 1427342018015 putative active site [active] 1427342018016 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342018017 PAS domain; Region: PAS_9; pfam13426 1427342018018 putative active site [active] 1427342018019 heme pocket [chemical binding]; other site 1427342018020 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342018021 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342018022 metal binding site [ion binding]; metal-binding site 1427342018023 active site 1427342018024 I-site; other site 1427342018025 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1427342018026 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 1427342018027 Part of AAA domain; Region: AAA_19; pfam13245 1427342018028 Family description; Region: UvrD_C_2; pfam13538 1427342018029 Predicted membrane protein [Function unknown]; Region: COG2510 1427342018030 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 1427342018031 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 1427342018032 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 1427342018033 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 1427342018034 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342018035 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_4; cd03795 1427342018036 putative ADP-binding pocket [chemical binding]; other site 1427342018037 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 1427342018038 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342018039 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 1427342018040 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342018041 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1427342018042 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1427342018043 Walker A/P-loop; other site 1427342018044 ATP binding site [chemical binding]; other site 1427342018045 Q-loop/lid; other site 1427342018046 ABC transporter signature motif; other site 1427342018047 Walker B; other site 1427342018048 D-loop; other site 1427342018049 H-loop/switch region; other site 1427342018050 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 1427342018051 putative carbohydrate binding site [chemical binding]; other site 1427342018052 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1427342018053 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1427342018054 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1427342018055 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1427342018056 Substrate binding site; other site 1427342018057 Cupin domain; Region: Cupin_2; cl17218 1427342018058 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 1427342018059 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 1427342018060 NADP-binding site; other site 1427342018061 homotetramer interface [polypeptide binding]; other site 1427342018062 substrate binding site [chemical binding]; other site 1427342018063 homodimer interface [polypeptide binding]; other site 1427342018064 active site 1427342018065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342018066 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 1427342018067 NAD(P) binding site [chemical binding]; other site 1427342018068 active site 1427342018069 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342018070 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1427342018071 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1427342018072 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1427342018073 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cd01635 1427342018074 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1427342018075 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342018076 S-adenosylmethionine binding site [chemical binding]; other site 1427342018077 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1427342018078 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1427342018079 Methyltransferase domain; Region: Methyltransf_11; pfam08241 1427342018080 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 1427342018081 conserverd hypothetical protein; Region: TIGR02448 1427342018082 Protein of unknown function (DUF2388); Region: DUF2388; pfam09498 1427342018083 Protein of unknown function (DUF2388); Region: DUF2388; pfam09498 1427342018084 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 1427342018085 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1427342018086 Predicted permeases [General function prediction only]; Region: COG0679 1427342018087 Protein of unknown function (DUF2388); Region: DUF2388; pfam09498 1427342018088 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 1427342018089 Citrate transporter; Region: CitMHS; pfam03600 1427342018090 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 1427342018091 peptide chain release factor-like protein; Reviewed; Region: prfH; PRK08179 1427342018092 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1427342018093 hypothetical protein; Reviewed; Region: PRK09588 1427342018094 release factor H-coupled RctB family protein; Region: release_rtcB; TIGR03073 1427342018095 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1427342018096 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 1427342018097 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1427342018098 PhoU domain; Region: PhoU; pfam01895 1427342018099 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1427342018100 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1427342018101 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1427342018102 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1427342018103 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342018104 citrate-proton symporter; Provisional; Region: PRK15075 1427342018105 putative substrate translocation pore; other site 1427342018106 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 1427342018107 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 1427342018108 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 1427342018109 glutamate/aspartate:proton symporter; Provisional; Region: gltP; PRK11283 1427342018110 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1427342018111 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; pfam08816 1427342018112 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342018113 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342018114 active site 1427342018115 phosphorylation site [posttranslational modification] 1427342018116 intermolecular recognition site; other site 1427342018117 dimerization interface [polypeptide binding]; other site 1427342018118 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342018119 Walker A motif; other site 1427342018120 ATP binding site [chemical binding]; other site 1427342018121 Walker B motif; other site 1427342018122 arginine finger; other site 1427342018123 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1427342018124 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1427342018125 dimerization interface [polypeptide binding]; other site 1427342018126 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1427342018127 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1427342018128 putative active site [active] 1427342018129 heme pocket [chemical binding]; other site 1427342018130 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342018131 dimer interface [polypeptide binding]; other site 1427342018132 phosphorylation site [posttranslational modification] 1427342018133 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342018134 ATP binding site [chemical binding]; other site 1427342018135 Mg2+ binding site [ion binding]; other site 1427342018136 G-X-G motif; other site 1427342018137 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1427342018138 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1427342018139 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1427342018140 amidase catalytic site [active] 1427342018141 Zn binding residues [ion binding]; other site 1427342018142 substrate binding site [chemical binding]; other site 1427342018143 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1427342018144 MarC family integral membrane protein; Region: MarC; cl00919 1427342018145 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1427342018146 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1427342018147 metal binding site [ion binding]; metal-binding site 1427342018148 active site 1427342018149 I-site; other site 1427342018150 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 1427342018151 putative catalytic site [active] 1427342018152 putative metal binding site [ion binding]; other site 1427342018153 putative phosphate binding site [ion binding]; other site 1427342018154 putative catalytic site [active] 1427342018155 putative phosphate binding site [ion binding]; other site 1427342018156 putative metal binding site [ion binding]; other site 1427342018157 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 1427342018158 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1427342018159 catalytic residues [active] 1427342018160 hinge region; other site 1427342018161 alpha helical domain; other site 1427342018162 Cytochrome c553 [Energy production and conversion]; Region: COG2863 1427342018163 Cytochrome c; Region: Cytochrom_C; cl11414 1427342018164 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 1427342018165 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1427342018166 G1 box; other site 1427342018167 GTP/Mg2+ binding site [chemical binding]; other site 1427342018168 Switch I region; other site 1427342018169 G2 box; other site 1427342018170 G3 box; other site 1427342018171 Switch II region; other site 1427342018172 G4 box; other site 1427342018173 G5 box; other site 1427342018174 DNA polymerase I; Provisional; Region: PRK05755 1427342018175 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1427342018176 active site 1427342018177 metal binding site 1 [ion binding]; metal-binding site 1427342018178 putative 5' ssDNA interaction site; other site 1427342018179 metal binding site 3; metal-binding site 1427342018180 metal binding site 2 [ion binding]; metal-binding site 1427342018181 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1427342018182 putative DNA binding site [nucleotide binding]; other site 1427342018183 putative metal binding site [ion binding]; other site 1427342018184 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 1427342018185 active site 1427342018186 catalytic site [active] 1427342018187 substrate binding site [chemical binding]; other site 1427342018188 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1427342018189 active site 1427342018190 DNA binding site [nucleotide binding] 1427342018191 catalytic site [active] 1427342018192 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 1427342018193 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 1427342018194 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 1427342018195 putative active site [active] 1427342018196 putative substrate binding site [chemical binding]; other site 1427342018197 ATP binding site [chemical binding]; other site 1427342018198 Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism]; Region: NrdA; COG0209 1427342018199 TSCPD domain; Region: TSCPD; pfam12637 1427342018200 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 1427342018201 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 1427342018202 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 1427342018203 active site 1427342018204 dimer interface [polypeptide binding]; other site 1427342018205 effector binding site; other site 1427342018206 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1427342018207 ABC-type Zn2+ transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: ZnuA; COG4531 1427342018208 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 1427342018209 metal binding site [ion binding]; metal-binding site 1427342018210 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1427342018211 Predicted transcriptional regulators [Transcription]; Region: COG1695 1427342018212 metal binding site 2 [ion binding]; metal-binding site 1427342018213 putative DNA binding helix; other site 1427342018214 metal binding site 1 [ion binding]; metal-binding site 1427342018215 dimer interface [polypeptide binding]; other site 1427342018216 structural Zn2+ binding site [ion binding]; other site 1427342018217 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 1427342018218 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1427342018219 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1427342018220 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 1427342018221 dimer interface [polypeptide binding]; other site 1427342018222 putative PBP binding regions; other site 1427342018223 ABC-ATPase subunit interface; other site 1427342018224 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 1427342018225 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 1427342018226 Walker A/P-loop; other site 1427342018227 ATP binding site [chemical binding]; other site 1427342018228 Q-loop/lid; other site 1427342018229 ABC transporter signature motif; other site 1427342018230 Walker B; other site 1427342018231 D-loop; other site 1427342018232 H-loop/switch region; other site 1427342018233 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 1427342018234 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1427342018235 dimer interface [polypeptide binding]; other site 1427342018236 conserved gate region; other site 1427342018237 ABC-ATPase subunit interface; other site 1427342018238 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1427342018239 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1427342018240 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 1427342018241 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 1427342018242 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 1427342018243 putative active site [active] 1427342018244 Isochorismatase family; Region: Isochorismatase; pfam00857 1427342018245 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 1427342018246 catalytic triad [active] 1427342018247 conserved cis-peptide bond; other site 1427342018248 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342018249 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342018250 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]; Region: COG3931 1427342018251 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 1427342018252 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1427342018253 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1427342018254 active site 1427342018255 phosphorylation site [posttranslational modification] 1427342018256 intermolecular recognition site; other site 1427342018257 dimerization interface [polypeptide binding]; other site 1427342018258 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 1427342018259 Walker A motif; other site 1427342018260 ATP binding site [chemical binding]; other site 1427342018261 Walker B motif; other site 1427342018262 arginine finger; other site 1427342018263 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1427342018264 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 1427342018265 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 1427342018266 dimer interface [polypeptide binding]; other site 1427342018267 phosphorylation site [posttranslational modification] 1427342018268 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 1427342018269 ATP binding site [chemical binding]; other site 1427342018270 Mg2+ binding site [ion binding]; other site 1427342018271 G-X-G motif; other site 1427342018272 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1427342018273 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1427342018274 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1427342018275 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 1427342018276 pyridoxamine kinase; Validated; Region: PRK05756 1427342018277 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 1427342018278 pyridoxal binding site [chemical binding]; other site 1427342018279 dimer interface [polypeptide binding]; other site 1427342018280 ATP binding site [chemical binding]; other site 1427342018281 Predicted membrane protein [Function unknown]; Region: COG1238 1427342018282 putative cation:proton antiport protein; Provisional; Region: PRK10669 1427342018283 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 1427342018284 TrkA-N domain; Region: TrkA_N; pfam02254 1427342018285 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 1427342018286 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342018287 classical (c) SDRs; Region: SDR_c; cd05233 1427342018288 NAD(P) binding site [chemical binding]; other site 1427342018289 active site 1427342018290 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1427342018291 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1427342018292 aminotransferase; Validated; Region: PRK07046 1427342018293 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 1427342018294 inhibitor-cofactor binding pocket; inhibition site 1427342018295 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1427342018296 catalytic residue [active] 1427342018297 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1427342018298 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1427342018299 NAD(P) binding site [chemical binding]; other site 1427342018300 active site 1427342018301 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1427342018302 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1427342018303 DNA-binding site [nucleotide binding]; DNA binding site 1427342018304 FCD domain; Region: FCD; pfam07729 1427342018305 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 1427342018306 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1427342018307 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1427342018308 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1427342018309 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 1427342018310 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342018311 putative substrate translocation pore; other site 1427342018312 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1427342018313 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1427342018314 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 1427342018315 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 1427342018316 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 1427342018317 Protein of unknown function (DUF1826); Region: DUF1826; pfam08856 1427342018318 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 1427342018319 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 1427342018320 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 1427342018321 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1427342018322 AMIN domain; Region: AMIN; pfam11741 1427342018323 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1427342018324 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 1427342018325 active site 1427342018326 metal binding site [ion binding]; metal-binding site 1427342018327 putative GTP cyclohydrolase; Provisional; Region: PRK13674 1427342018328 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1427342018329 Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed...; Region: LbH_gamma_CA; cd00710 1427342018330 trimer interface [polypeptide binding]; other site 1427342018331 active site 1427342018332 dihydroorotase; Reviewed; Region: PRK09236 1427342018333 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 1427342018334 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 1427342018335 active site 1427342018336 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1427342018337 Beta-lactamase; Region: Beta-lactamase; pfam00144 1427342018338 Uncharacterized conserved protein [Function unknown]; Region: COG4729 1427342018339 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 1427342018340 DctM-like transporters; Region: DctM; pfam06808 1427342018341 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1427342018342 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1427342018343 substrate binding pocket [chemical binding]; other site 1427342018344 membrane-bound complex binding site; other site 1427342018345 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 1427342018346 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 1427342018347 S-adenosylmethionine binding site [chemical binding]; other site 1427342018348 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 1427342018349 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like; Region: HAD-SF-IB; TIGR01488 1427342018350 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1427342018351 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342018352 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342018353 Cytochrome P450; Region: p450; cl12078 1427342018354 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1427342018355 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342018356 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1427342018357 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342018358 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1427342018359 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1427342018360 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 1427342018361 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 1427342018362 putative substrate translocation pore; other site 1427342018363 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 1427342018364 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 1427342018365 glutaminase active site [active] 1427342018366 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 1427342018367 dimer interface [polypeptide binding]; other site 1427342018368 active site 1427342018369 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 1427342018370 dimer interface [polypeptide binding]; other site 1427342018371 active site 1427342018372 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 1427342018373 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 1427342018374 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 1427342018375 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1427342018376 Peptidase family M23; Region: Peptidase_M23; pfam01551 1427342018377 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 1427342018378 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1427342018379 Substrate binding site; other site 1427342018380 Mg++ binding site; other site 1427342018381 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 1427342018382 active site 1427342018383 substrate binding site [chemical binding]; other site 1427342018384 CoA binding site [chemical binding]; other site 1427342018385 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 1427342018386 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1427342018387 gamma subunit interface [polypeptide binding]; other site 1427342018388 epsilon subunit interface [polypeptide binding]; other site 1427342018389 LBP interface [polypeptide binding]; other site 1427342018390 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1427342018391 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1427342018392 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 1427342018393 alpha subunit interaction interface [polypeptide binding]; other site 1427342018394 Walker A motif; other site 1427342018395 ATP binding site [chemical binding]; other site 1427342018396 Walker B motif; other site 1427342018397 inhibitor binding site; inhibition site 1427342018398 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1427342018399 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1427342018400 core domain interface [polypeptide binding]; other site 1427342018401 delta subunit interface [polypeptide binding]; other site 1427342018402 epsilon subunit interface [polypeptide binding]; other site 1427342018403 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1427342018404 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1427342018405 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 1427342018406 beta subunit interaction interface [polypeptide binding]; other site 1427342018407 Walker A motif; other site 1427342018408 ATP binding site [chemical binding]; other site 1427342018409 Walker B motif; other site 1427342018410 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1427342018411 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1427342018412 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1427342018413 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1427342018414 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 1427342018415 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 1427342018416 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1427342018417 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 1427342018418 F0F1 ATP synthase subunit I; Validated; Region: PRK05760 1427342018419 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 1427342018420 ParB-like nuclease domain; Region: ParBc; pfam02195 1427342018421 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1427342018422 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342018423 P-loop; other site 1427342018424 Magnesium ion binding site [ion binding]; other site 1427342018425 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 1427342018426 Magnesium ion binding site [ion binding]; other site 1427342018427 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1427342018428 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1427342018429 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1427342018430 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1427342018431 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1427342018432 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1427342018433 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1427342018434 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1427342018435 G1 box; other site 1427342018436 GTP/Mg2+ binding site [chemical binding]; other site 1427342018437 Switch I region; other site 1427342018438 G2 box; other site 1427342018439 Switch II region; other site 1427342018440 G3 box; other site 1427342018441 G4 box; other site 1427342018442 G5 box; other site 1427342018443 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1427342018444 membrane protein insertase; Provisional; Region: PRK01318 1427342018445 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1427342018446 ribonuclease P; Reviewed; Region: rnpA; PRK00396 1427342018447 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399