-- dump date 20140619_143940 -- class Genbank::misc_feature -- table misc_feature_note -- id note 420662000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 420662000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 420662000003 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 420662000004 Walker A motif; other site 420662000005 ATP binding site [chemical binding]; other site 420662000006 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; cl17189 420662000007 Walker B motif; other site 420662000008 arginine finger; other site 420662000009 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 420662000010 DnaA box-binding interface [nucleotide binding]; other site 420662000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 420662000012 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 420662000013 putative DNA binding surface [nucleotide binding]; other site 420662000014 dimer interface [polypeptide binding]; other site 420662000015 beta-clamp/clamp loader binding surface; other site 420662000016 beta-clamp/translesion DNA polymerase binding surface; other site 420662000017 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 420662000018 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 420662000019 ATP binding site [chemical binding]; other site 420662000020 Mg2+ binding site [ion binding]; other site 420662000021 G-X-G motif; other site 420662000022 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 420662000023 anchoring element; other site 420662000024 dimer interface [polypeptide binding]; other site 420662000025 ATP binding site [chemical binding]; other site 420662000026 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 420662000027 active site 420662000028 putative metal-binding site [ion binding]; other site 420662000029 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 420662000030 HsdM N-terminal domain; Region: HsdM_N; pfam12161 420662000031 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 420662000032 Methyltransferase domain; Region: Methyltransf_26; pfam13659 420662000033 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 420662000034 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 420662000035 Predicted ATPase [General function prediction only]; Region: COG4637 420662000036 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 420662000037 Walker A/P-loop; other site 420662000038 ATP binding site [chemical binding]; other site 420662000039 Domain of unknown function (DUF4276); Region: DUF4276; pfam14103 420662000040 Fic family protein [Function unknown]; Region: COG3177 420662000041 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 420662000042 Fic/DOC family; Region: Fic; pfam02661 420662000043 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 420662000044 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 420662000045 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 420662000046 ATP binding site [chemical binding]; other site 420662000047 putative Mg++ binding site [ion binding]; other site 420662000048 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 420662000049 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662000050 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 420662000051 ligand binding site [chemical binding]; other site 420662000052 flexible hinge region; other site 420662000053 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 420662000054 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662000055 Predicted membrane protein [Function unknown]; Region: COG2259 420662000056 putative adenylate-forming enzyme; Region: aden_form_hyp; TIGR02304 420662000057 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 420662000058 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 420662000059 Ligand Binding Site [chemical binding]; other site 420662000060 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 420662000061 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 420662000062 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662000063 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 420662000064 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_24; cd09012 420662000065 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 420662000066 YCII-related domain; Region: YCII; cl00999 420662000067 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 420662000068 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 420662000069 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662000070 catalytic residue [active] 420662000071 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 420662000072 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 420662000073 non-specific DNA binding site [nucleotide binding]; other site 420662000074 salt bridge; other site 420662000075 sequence-specific DNA binding site [nucleotide binding]; other site 420662000076 serine O-acetyltransferase; Region: cysE; TIGR01172 420662000077 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 420662000078 trimer interface [polypeptide binding]; other site 420662000079 active site 420662000080 substrate binding site [chemical binding]; other site 420662000081 CoA binding site [chemical binding]; other site 420662000082 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 420662000083 active site residue [active] 420662000084 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 420662000085 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 420662000086 homodimer interface [polypeptide binding]; other site 420662000087 substrate-cofactor binding pocket; other site 420662000088 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662000089 catalytic residue [active] 420662000090 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 420662000091 dimer interface [polypeptide binding]; other site 420662000092 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662000093 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 420662000094 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 420662000095 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 420662000096 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; cl15270 420662000097 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662000098 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662000099 short chain dehydrogenase; Validated; Region: PRK08264 420662000100 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662000101 NAD(P) binding site [chemical binding]; other site 420662000102 active site 420662000103 Paraquat-inducible protein A; Region: PqiA; pfam04403 420662000104 Paraquat-inducible protein A; Region: PqiA; pfam04403 420662000105 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 420662000106 mce related protein; Region: MCE; pfam02470 420662000107 mce related protein; Region: MCE; pfam02470 420662000108 mce related protein; Region: MCE; pfam02470 420662000109 Protein of unknown function (DUF330); Region: DUF330; pfam03886 420662000110 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 420662000111 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 420662000112 Predicted integral membrane protein [Function unknown]; Region: COG0392 420662000113 cardiolipin synthase 2; Provisional; Region: PRK11263 420662000114 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 420662000115 putative active site [active] 420662000116 catalytic site [active] 420662000117 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 420662000118 putative active site [active] 420662000119 catalytic site [active] 420662000120 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 420662000121 putative catalytic site [active] 420662000122 putative metal binding site [ion binding]; other site 420662000123 putative phosphate binding site [ion binding]; other site 420662000124 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 420662000125 active site 420662000126 catalytic site [active] 420662000127 substrate binding site [chemical binding]; other site 420662000128 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 420662000129 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662000130 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 420662000131 DNA binding residues [nucleotide binding] 420662000132 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 420662000133 putative active site [active] 420662000134 Zn binding site [ion binding]; other site 420662000135 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662000136 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662000137 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662000138 putative hydrolase; Provisional; Region: PRK11460 420662000139 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 420662000140 NnrU protein; Region: NnrU; pfam07298 420662000141 SWIB/MDM2 domain; Region: SWIB; pfam02201 420662000142 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 420662000143 MarR family; Region: MarR; pfam01047 420662000144 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 420662000145 Membrane protein of unknown function; Region: DUF360; pfam04020 420662000146 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 420662000147 Peptidase family M48; Region: Peptidase_M48; cl12018 420662000148 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 420662000149 trimer interface [polypeptide binding]; other site 420662000150 dimer interface [polypeptide binding]; other site 420662000151 putative active site [active] 420662000152 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 420662000153 O-Antigen ligase; Region: Wzy_C; pfam04932 420662000154 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 420662000155 Pilin (bacterial filament); Region: Pilin; pfam00114 420662000156 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 420662000157 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 420662000158 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 420662000159 phosphopeptide binding site; other site 420662000160 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; cl00062 420662000161 phosphopeptide binding site; other site 420662000162 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 420662000163 active site 420662000164 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662000165 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662000166 active site 420662000167 ATP binding site [chemical binding]; other site 420662000168 substrate binding site [chemical binding]; other site 420662000169 activation loop (A-loop); other site 420662000170 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 420662000171 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 420662000172 CoA binding domain; Region: CoA_binding; smart00881 420662000173 CoA-ligase; Region: Ligase_CoA; pfam00549 420662000174 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 420662000175 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 420662000176 CoA-ligase; Region: Ligase_CoA; pfam00549 420662000177 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 420662000178 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 420662000179 RecX family; Region: RecX; cl00936 420662000180 recombinase A; Provisional; Region: recA; PRK09354 420662000181 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 420662000182 hexamer interface [polypeptide binding]; other site 420662000183 Walker A motif; other site 420662000184 ATP binding site [chemical binding]; other site 420662000185 Walker B motif; other site 420662000186 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 420662000187 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 420662000188 active site 420662000189 phosphorylation site [posttranslational modification] 420662000190 intermolecular recognition site; other site 420662000191 dimerization interface [polypeptide binding]; other site 420662000192 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 420662000193 DNA binding site [nucleotide binding] 420662000194 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 420662000195 HAMP domain; Region: HAMP; pfam00672 420662000196 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 420662000197 dimer interface [polypeptide binding]; other site 420662000198 phosphorylation site [posttranslational modification] 420662000199 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 420662000200 ATP binding site [chemical binding]; other site 420662000201 Mg2+ binding site [ion binding]; other site 420662000202 G-X-G motif; other site 420662000203 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 420662000204 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 420662000205 active site 420662000206 nucleophile elbow; other site 420662000207 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 420662000208 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 420662000209 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 420662000210 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 420662000211 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 420662000212 rod shape-determining protein MreC; Provisional; Region: PRK13922 420662000213 rod shape-determining protein MreC; Region: MreC; pfam04085 420662000214 rod shape-determining protein MreB; Provisional; Region: PRK13927 420662000215 MreB and similar proteins; Region: MreB_like; cd10225 420662000216 nucleotide binding site [chemical binding]; other site 420662000217 Mg binding site [ion binding]; other site 420662000218 putative protofilament interaction site [polypeptide binding]; other site 420662000219 RodZ interaction site [polypeptide binding]; other site 420662000220 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 420662000221 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 420662000222 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 420662000223 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 420662000224 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 420662000225 GatB domain; Region: GatB_Yqey; smart00845 420662000226 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662000227 active site 420662000228 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 420662000229 putative active site [active] 420662000230 putative catalytic site [active] 420662000231 putative DNA binding site [nucleotide binding]; other site 420662000232 putative phosphate binding site [ion binding]; other site 420662000233 metal binding site A [ion binding]; metal-binding site 420662000234 putative AP binding site [nucleotide binding]; other site 420662000235 putative metal binding site B [ion binding]; other site 420662000236 Acyltransferase family; Region: Acyl_transf_3; pfam01757 420662000237 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662000238 Peptidase family M48; Region: Peptidase_M48; pfam01435 420662000239 muropeptide transporter; Validated; Region: ampG; cl17669 420662000240 muropeptide transporter; Validated; Region: ampG; cl17669 420662000241 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 420662000242 active site 420662000243 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 420662000244 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662000245 GAF domain; Region: GAF; pfam01590 420662000246 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 420662000247 PAS domain; Region: PAS_9; pfam13426 420662000248 putative active site [active] 420662000249 heme pocket [chemical binding]; other site 420662000250 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 420662000251 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 420662000252 putative active site [active] 420662000253 heme pocket [chemical binding]; other site 420662000254 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 420662000255 heme pocket [chemical binding]; other site 420662000256 putative active site [active] 420662000257 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662000258 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 420662000259 dimer interface [polypeptide binding]; other site 420662000260 phosphorylation site [posttranslational modification] 420662000261 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 420662000262 ATP binding site [chemical binding]; other site 420662000263 Mg2+ binding site [ion binding]; other site 420662000264 G-X-G motif; other site 420662000265 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 420662000266 Response regulator receiver domain; Region: Response_reg; pfam00072 420662000267 active site 420662000268 phosphorylation site [posttranslational modification] 420662000269 intermolecular recognition site; other site 420662000270 dimerization interface [polypeptide binding]; other site 420662000271 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 420662000272 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 420662000273 putative catalytic residue [active] 420662000274 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662000275 CHAT domain; Region: CHAT; pfam12770 420662000276 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 420662000277 ligand binding site [chemical binding]; other site 420662000278 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 420662000279 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 420662000280 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 420662000281 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 420662000282 RNA polymerase sigma factor; Provisional; Region: PRK12513 420662000283 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662000284 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 420662000285 DNA binding residues [nucleotide binding] 420662000286 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 420662000287 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 420662000288 metal ion-dependent adhesion site (MIDAS); other site 420662000289 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 420662000290 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 420662000291 ATP binding site [chemical binding]; other site 420662000292 putative Mg++ binding site [ion binding]; other site 420662000293 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 420662000294 nucleotide binding region [chemical binding]; other site 420662000295 ATP-binding site [chemical binding]; other site 420662000296 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 420662000297 HRDC domain; Region: HRDC; pfam00570 420662000298 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 420662000299 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 420662000300 putative ion selectivity filter; other site 420662000301 putative pore gating glutamate residue; other site 420662000302 putative H+/Cl- coupling transport residue; other site 420662000303 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 420662000304 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 420662000305 dimer interface [polypeptide binding]; other site 420662000306 ssDNA binding site [nucleotide binding]; other site 420662000307 tetramer (dimer of dimers) interface [polypeptide binding]; other site 420662000308 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 420662000309 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 420662000310 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 420662000311 TrkA-N domain; Region: TrkA_N; pfam02254 420662000312 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 420662000313 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 420662000314 substrate binding pocket [chemical binding]; other site 420662000315 membrane-bound complex binding site; other site 420662000316 hinge residues; other site 420662000317 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 420662000318 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 420662000319 substrate binding pocket [chemical binding]; other site 420662000320 membrane-bound complex binding site; other site 420662000321 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 420662000322 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 420662000323 active site 420662000324 dimer interface [polypeptide binding]; other site 420662000325 non-prolyl cis peptide bond; other site 420662000326 insertion regions; other site 420662000327 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662000328 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 420662000329 dimer interface [polypeptide binding]; other site 420662000330 conserved gate region; other site 420662000331 putative PBP binding loops; other site 420662000332 ABC-ATPase subunit interface; other site 420662000333 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 420662000334 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662000335 Walker A/P-loop; other site 420662000336 ATP binding site [chemical binding]; other site 420662000337 Q-loop/lid; other site 420662000338 ABC transporter signature motif; other site 420662000339 Walker B; other site 420662000340 D-loop; other site 420662000341 H-loop/switch region; other site 420662000342 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 420662000343 catalytic residues [active] 420662000344 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 420662000345 Serine hydrolase; Region: Ser_hydrolase; pfam06821 420662000346 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662000347 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 420662000348 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 420662000349 dimer interface [polypeptide binding]; other site 420662000350 decamer (pentamer of dimers) interface [polypeptide binding]; other site 420662000351 catalytic triad [active] 420662000352 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 420662000353 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 420662000354 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 420662000355 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 420662000356 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 420662000357 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 420662000358 dimer interface [polypeptide binding]; other site 420662000359 conserved gate region; other site 420662000360 putative PBP binding loops; other site 420662000361 ABC-ATPase subunit interface; other site 420662000362 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 420662000363 dimer interface [polypeptide binding]; other site 420662000364 conserved gate region; other site 420662000365 putative PBP binding loops; other site 420662000366 ABC-ATPase subunit interface; other site 420662000367 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 420662000368 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 420662000369 Walker A/P-loop; other site 420662000370 ATP binding site [chemical binding]; other site 420662000371 Q-loop/lid; other site 420662000372 ABC transporter signature motif; other site 420662000373 Walker B; other site 420662000374 D-loop; other site 420662000375 H-loop/switch region; other site 420662000376 TOBE-like domain; Region: TOBE_3; pfam12857 420662000377 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 420662000378 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662000379 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 420662000380 substrate binding site [chemical binding]; other site 420662000381 dimerization interface [polypeptide binding]; other site 420662000382 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 420662000383 Part of AAA domain; Region: AAA_19; pfam13245 420662000384 Family description; Region: UvrD_C_2; pfam13538 420662000385 Predicted permeases [General function prediction only]; Region: COG0679 420662000386 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662000387 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662000388 trimer interface [polypeptide binding]; other site 420662000389 eyelet of channel; other site 420662000390 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 420662000391 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 420662000392 substrate binding pocket [chemical binding]; other site 420662000393 membrane-bound complex binding site; other site 420662000394 hinge residues; other site 420662000395 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 420662000396 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 420662000397 dimer interface [polypeptide binding]; other site 420662000398 conserved gate region; other site 420662000399 putative PBP binding loops; other site 420662000400 ABC-ATPase subunit interface; other site 420662000401 primosome assembly protein PriA; Validated; Region: PRK05580 420662000402 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 420662000403 ATP binding site [chemical binding]; other site 420662000404 putative Mg++ binding site [ion binding]; other site 420662000405 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 420662000406 substrate binding site [chemical binding]; other site 420662000407 active site 420662000408 DNA-binding response regulator CreB; Provisional; Region: PRK11083 420662000409 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 420662000410 active site 420662000411 phosphorylation site [posttranslational modification] 420662000412 intermolecular recognition site; other site 420662000413 dimerization interface [polypeptide binding]; other site 420662000414 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 420662000415 DNA binding site [nucleotide binding] 420662000416 sensory histidine kinase CreC; Provisional; Region: PRK11100 420662000417 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 420662000418 dimer interface [polypeptide binding]; other site 420662000419 phosphorylation site [posttranslational modification] 420662000420 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 420662000421 ATP binding site [chemical binding]; other site 420662000422 Mg2+ binding site [ion binding]; other site 420662000423 G-X-G motif; other site 420662000424 YCII-related domain; Region: YCII; cl00999 420662000425 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662000426 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662000427 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 420662000428 putative dimerization interface [polypeptide binding]; other site 420662000429 Domain of unknown function (DUF897); Region: DUF897; pfam05982 420662000430 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 420662000431 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 420662000432 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 420662000433 metal ion-dependent adhesion site (MIDAS); other site 420662000434 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 420662000435 Transglycosylase; Region: Transgly; pfam00912 420662000436 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662000437 NAD(P) binding site [chemical binding]; other site 420662000438 active site 420662000439 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 420662000440 Repair protein; Region: Repair_PSII; pfam04536 420662000441 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 420662000442 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 420662000443 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 420662000444 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 420662000445 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 420662000446 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 420662000447 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 420662000448 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 420662000449 Walker A/P-loop; other site 420662000450 ATP binding site [chemical binding]; other site 420662000451 Q-loop/lid; other site 420662000452 ABC transporter signature motif; other site 420662000453 Walker B; other site 420662000454 D-loop; other site 420662000455 H-loop/switch region; other site 420662000456 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 420662000457 OstA-like protein; Region: OstA; pfam03968 420662000458 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 420662000459 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 420662000460 catalytic residues [active] 420662000461 hinge region; other site 420662000462 alpha helical domain; other site 420662000463 Sporulation related domain; Region: SPOR; pfam05036 420662000464 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 420662000465 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 420662000466 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 420662000467 active site 420662000468 HIGH motif; other site 420662000469 KMSK motif region; other site 420662000470 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 420662000471 tRNA binding surface [nucleotide binding]; other site 420662000472 anticodon binding site; other site 420662000473 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662000474 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662000475 active site 420662000476 ATP binding site [chemical binding]; other site 420662000477 substrate binding site [chemical binding]; other site 420662000478 activation loop (A-loop); other site 420662000479 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 420662000480 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662000481 ligand binding site [chemical binding]; other site 420662000482 psiF repeat; Region: PsiF_repeat; pfam07769 420662000483 psiF repeat; Region: PsiF_repeat; pfam07769 420662000484 Protein of unknown function (DUF3047); Region: DUF3047; pfam11249 420662000485 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662000486 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662000487 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 420662000488 putative effector binding pocket; other site 420662000489 dimerization interface [polypeptide binding]; other site 420662000490 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 420662000491 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 420662000492 motif II; other site 420662000493 malate synthase A; Region: malate_syn_A; TIGR01344 420662000494 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 420662000495 active site 420662000496 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 420662000497 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662000498 RNA polymerase sigma factor; Provisional; Region: PRK12537 420662000499 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662000500 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 420662000501 DNA binding residues [nucleotide binding] 420662000502 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 420662000503 Anti-sigma-K factor rskA; Region: RskA; pfam10099 420662000504 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 420662000505 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 420662000506 active site 420662000507 Zn binding site [ion binding]; other site 420662000508 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 420662000509 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 420662000510 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662000511 Walker A motif; other site 420662000512 ATP binding site [chemical binding]; other site 420662000513 Walker B motif; other site 420662000514 arginine finger; other site 420662000515 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 420662000516 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662000517 Walker A motif; other site 420662000518 ATP binding site [chemical binding]; other site 420662000519 Walker B motif; other site 420662000520 arginine finger; other site 420662000521 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 420662000522 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 420662000523 OmpA family; Region: OmpA; pfam00691 420662000524 ligand binding site [chemical binding]; other site 420662000525 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 420662000526 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 420662000527 substrate binding pocket [chemical binding]; other site 420662000528 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 420662000529 B12 binding site [chemical binding]; other site 420662000530 cobalt ligand [ion binding]; other site 420662000531 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 420662000532 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 420662000533 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 420662000534 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 420662000535 Walker A motif; other site 420662000536 ATP binding site [chemical binding]; other site 420662000537 Walker B motif; other site 420662000538 arginine finger; other site 420662000539 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 420662000540 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 420662000541 Nitrogen regulatory protein P-II; Region: P-II; smart00938 420662000542 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 420662000543 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 420662000544 Glutamate-cysteine ligase; Region: GshA; pfam08886 420662000545 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 420662000546 potassium uptake protein; Region: kup; TIGR00794 420662000547 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662000548 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662000549 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662000550 acyl-CoA synthetase; Validated; Region: PRK06188 420662000551 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662000552 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 420662000553 acyl-activating enzyme (AAE) consensus motif; other site 420662000554 acyl-activating enzyme (AAE) consensus motif; other site 420662000555 putative AMP binding site [chemical binding]; other site 420662000556 putative active site [active] 420662000557 putative CoA binding site [chemical binding]; other site 420662000558 lipid-transfer protein; Provisional; Region: PRK08256 420662000559 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 420662000560 active site 420662000561 Benzoate membrane transport protein; Region: BenE; pfam03594 420662000562 benzoate transporter; Region: benE; TIGR00843 420662000563 glutathione synthetase; Provisional; Region: PRK05246 420662000564 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 420662000565 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 420662000566 ABC transporter ATPase component; Reviewed; Region: PRK11147 420662000567 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662000568 Walker A/P-loop; other site 420662000569 ATP binding site [chemical binding]; other site 420662000570 Q-loop/lid; other site 420662000571 ABC transporter signature motif; other site 420662000572 Walker B; other site 420662000573 D-loop; other site 420662000574 H-loop/switch region; other site 420662000575 ABC transporter; Region: ABC_tran_2; pfam12848 420662000576 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662000577 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 420662000578 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662000579 DNA-binding site [nucleotide binding]; DNA binding site 420662000580 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 420662000581 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662000582 homodimer interface [polypeptide binding]; other site 420662000583 catalytic residue [active] 420662000584 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662000585 EamA-like transporter family; Region: EamA; pfam00892 420662000586 EamA-like transporter family; Region: EamA; pfam00892 420662000587 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 420662000588 aspartate racemase; Region: asp_race; TIGR00035 420662000589 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 420662000590 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 420662000591 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662000592 homodimer interface [polypeptide binding]; other site 420662000593 catalytic residue [active] 420662000594 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 420662000595 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 420662000596 Coenzyme A binding pocket [chemical binding]; other site 420662000597 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 420662000598 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 420662000599 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 420662000600 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 420662000601 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 420662000602 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 420662000603 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 420662000604 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 420662000605 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 420662000606 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 420662000607 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 420662000608 beta subunit interaction interface [polypeptide binding]; other site 420662000609 Walker A motif; other site 420662000610 ATP binding site [chemical binding]; other site 420662000611 Walker B motif; other site 420662000612 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 420662000613 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 420662000614 core domain interface [polypeptide binding]; other site 420662000615 delta subunit interface [polypeptide binding]; other site 420662000616 epsilon subunit interface [polypeptide binding]; other site 420662000617 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 420662000618 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 420662000619 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 420662000620 alpha subunit interaction interface [polypeptide binding]; other site 420662000621 Walker A motif; other site 420662000622 ATP binding site [chemical binding]; other site 420662000623 Walker B motif; other site 420662000624 inhibitor binding site; inhibition site 420662000625 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 420662000626 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 420662000627 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 420662000628 gamma subunit interface [polypeptide binding]; other site 420662000629 epsilon subunit interface [polypeptide binding]; other site 420662000630 LBP interface [polypeptide binding]; other site 420662000631 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 420662000632 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 420662000633 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 420662000634 Phosphotransferase enzyme family; Region: APH; pfam01636 420662000635 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 420662000636 OstA-like protein; Region: OstA; cl00844 420662000637 Organic solvent tolerance protein; Region: OstA_C; pfam04453 420662000638 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 420662000639 SurA N-terminal domain; Region: SurA_N; pfam09312 420662000640 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 420662000641 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 420662000642 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 420662000643 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 420662000644 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 420662000645 putative RNAase interaction site [polypeptide binding]; other site 420662000646 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 420662000647 active site 420662000648 barstar interaction site; other site 420662000649 malic enzyme; Reviewed; Region: PRK12862 420662000650 Malate dehydrogenase enzyme; Region: Malate_DH; pfam12434 420662000651 Malic enzyme, N-terminal domain; Region: malic; pfam00390 420662000652 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 420662000653 putative NAD(P) binding site [chemical binding]; other site 420662000654 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 420662000655 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 420662000656 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 420662000657 putative active site [active] 420662000658 heme pocket [chemical binding]; other site 420662000659 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 420662000660 dimer interface [polypeptide binding]; other site 420662000661 phosphorylation site [posttranslational modification] 420662000662 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 420662000663 ATP binding site [chemical binding]; other site 420662000664 Mg2+ binding site [ion binding]; other site 420662000665 G-X-G motif; other site 420662000666 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 420662000667 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 420662000668 active site 420662000669 phosphorylation site [posttranslational modification] 420662000670 intermolecular recognition site; other site 420662000671 dimerization interface [polypeptide binding]; other site 420662000672 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 420662000673 dimerization interface [polypeptide binding]; other site 420662000674 DNA binding residues [nucleotide binding] 420662000675 thiamine monophosphate kinase; Provisional; Region: PRK05731 420662000676 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 420662000677 ATP binding site [chemical binding]; other site 420662000678 dimerization interface [polypeptide binding]; other site 420662000679 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 420662000680 tetramer interfaces [polypeptide binding]; other site 420662000681 binuclear metal-binding site [ion binding]; other site 420662000682 Competence-damaged protein; Region: CinA; pfam02464 420662000683 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 420662000684 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 420662000685 putative ligand binding site [chemical binding]; other site 420662000686 NAD binding site [chemical binding]; other site 420662000687 dimerization interface [polypeptide binding]; other site 420662000688 catalytic site [active] 420662000689 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 420662000690 dimerization interface [polypeptide binding]; other site 420662000691 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662000692 metal binding site [ion binding]; metal-binding site 420662000693 active site 420662000694 I-site; other site 420662000695 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 420662000696 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 420662000697 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 420662000698 Lipopolysaccharide-assembly; Region: LptE; cl01125 420662000699 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 420662000700 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 420662000701 HIGH motif; other site 420662000702 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 420662000703 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 420662000704 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 420662000705 active site 420662000706 KMSKS motif; other site 420662000707 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 420662000708 tRNA binding surface [nucleotide binding]; other site 420662000709 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662000710 TolR protein; Region: tolR; TIGR02801 420662000711 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 420662000712 dihydrodipicolinate reductase; Provisional; Region: PRK00048 420662000713 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 420662000714 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 420662000715 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 420662000716 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 420662000717 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 420662000718 ferric uptake regulator; Provisional; Region: fur; PRK09462 420662000719 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 420662000720 metal binding site 2 [ion binding]; metal-binding site 420662000721 putative DNA binding helix; other site 420662000722 metal binding site 1 [ion binding]; metal-binding site 420662000723 dimer interface [polypeptide binding]; other site 420662000724 structural Zn2+ binding site [ion binding]; other site 420662000725 HPr kinase/phosphorylase; Provisional; Region: PRK05428 420662000726 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 420662000727 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 420662000728 Hpr binding site; other site 420662000729 active site 420662000730 homohexamer subunit interaction site [polypeptide binding]; other site 420662000731 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 420662000732 active site 420662000733 phosphorylation site [posttranslational modification] 420662000734 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 420662000735 30S subunit binding site; other site 420662000736 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 420662000737 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 420662000738 Cl binding site [ion binding]; other site 420662000739 oligomer interface [polypeptide binding]; other site 420662000740 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 420662000741 putative substrate translocation pore; other site 420662000742 SnoaL-like domain; Region: SnoaL_2; pfam12680 420662000743 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662000744 short chain dehydrogenase; Provisional; Region: PRK06101 420662000745 NAD(P) binding site [chemical binding]; other site 420662000746 active site 420662000747 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 420662000748 MFS/sugar transport protein; Region: MFS_2; pfam13347 420662000749 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 420662000750 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 420662000751 S-adenosylmethionine binding site [chemical binding]; other site 420662000752 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 420662000753 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 420662000754 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 420662000755 hydroxyglutarate oxidase; Provisional; Region: PRK11728 420662000756 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 420662000757 catalytic residues [active] 420662000758 dimer interface [polypeptide binding]; other site 420662000759 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 420662000760 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 420662000761 DNA binding residues [nucleotide binding] 420662000762 B12 binding domain; Region: B12-binding_2; pfam02607 420662000763 B12 binding domain; Region: B12-binding; pfam02310 420662000764 B12 binding site [chemical binding]; other site 420662000765 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662000766 dinuclear metal binding motif [ion binding]; other site 420662000767 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 420662000768 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 420662000769 active site 420662000770 nucleotide binding site [chemical binding]; other site 420662000771 HIGH motif; other site 420662000772 KMSKS motif; other site 420662000773 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 420662000774 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 420662000775 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 420662000776 metal binding triad; other site 420662000777 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 420662000778 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 420662000779 metal binding triad [ion binding]; metal-binding site 420662000780 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 420662000781 Predicted membrane protein [Function unknown]; Region: COG3164 420662000782 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 420662000783 nitrilase; Region: PLN02798 420662000784 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 420662000785 putative active site [active] 420662000786 catalytic triad [active] 420662000787 dimer interface [polypeptide binding]; other site 420662000788 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 420662000789 hypothetical protein; Provisional; Region: PRK06996 420662000790 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. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 420662000791 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 420662000792 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 420662000793 spermidine synthase; Provisional; Region: PRK03612 420662000794 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 420662000795 S-adenosylmethionine binding site [chemical binding]; other site 420662000796 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 420662000797 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 420662000798 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 420662000799 tartrate dehydrogenase; Region: TTC; TIGR02089 420662000800 proline aminopeptidase P II; Provisional; Region: PRK10879 420662000801 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 420662000802 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 420662000803 active site 420662000804 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 420662000805 voltage-dependent potassium channel beta subunit, animal; Region: Kv_beta; TIGR01293 420662000806 active site 420662000807 catalytic tetrad [active] 420662000808 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 420662000809 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 420662000810 Substrate binding site; other site 420662000811 metal-binding site 420662000812 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 420662000813 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 420662000814 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 420662000815 TPP-binding site [chemical binding]; other site 420662000816 dimer interface [polypeptide binding]; other site 420662000817 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 420662000818 PYR/PP interface [polypeptide binding]; other site 420662000819 dimer interface [polypeptide binding]; other site 420662000820 TPP binding site [chemical binding]; other site 420662000821 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 420662000822 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 420662000823 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 420662000824 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 420662000825 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 420662000826 active site 420662000827 catalytic triad [active] 420662000828 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 420662000829 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 420662000830 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 420662000831 DNA topoisomerase III; Validated; Region: PRK08173 420662000832 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 420662000833 active site 420662000834 putative interdomain interaction site [polypeptide binding]; other site 420662000835 putative metal-binding site [ion binding]; other site 420662000836 putative nucleotide binding site [chemical binding]; other site 420662000837 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 420662000838 domain I; other site 420662000839 DNA binding groove [nucleotide binding] 420662000840 phosphate binding site [ion binding]; other site 420662000841 domain II; other site 420662000842 domain III; other site 420662000843 nucleotide binding site [chemical binding]; other site 420662000844 catalytic site [active] 420662000845 domain IV; other site 420662000846 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 420662000847 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 420662000848 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 420662000849 Ligand Binding Site [chemical binding]; other site 420662000850 Membrane transport protein; Region: Mem_trans; cl09117 420662000851 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 420662000852 putative catalytic cysteine [active] 420662000853 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 420662000854 Ligand Binding Site [chemical binding]; other site 420662000855 LemA family; Region: LemA; cl00742 420662000856 16S rRNA methyltransferase B; Provisional; Region: PRK10901 420662000857 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 420662000858 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 420662000859 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 420662000860 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 420662000861 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 420662000862 dimerization interface [polypeptide binding]; other site 420662000863 PAS domain; Region: PAS_8; pfam13188 420662000864 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 420662000865 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 420662000866 dimer interface [polypeptide binding]; other site 420662000867 phosphorylation site [posttranslational modification] 420662000868 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 420662000869 ATP binding site [chemical binding]; other site 420662000870 Mg2+ binding site [ion binding]; other site 420662000871 G-X-G motif; other site 420662000872 Response regulator receiver domain; Region: Response_reg; pfam00072 420662000873 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 420662000874 active site 420662000875 phosphorylation site [posttranslational modification] 420662000876 intermolecular recognition site; other site 420662000877 dimerization interface [polypeptide binding]; other site 420662000878 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 420662000879 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 420662000880 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 420662000881 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 420662000882 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 420662000883 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 420662000884 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 420662000885 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 420662000886 Protein export membrane protein; Region: SecD_SecF; pfam02355 420662000887 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 420662000888 Protein of unknown function (DUF494); Region: DUF494; pfam04361 420662000889 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 420662000890 DNA protecting protein DprA; Region: dprA; TIGR00732 420662000891 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 420662000892 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 420662000893 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 420662000894 active site 420662000895 catalytic residues [active] 420662000896 metal binding site [ion binding]; metal-binding site 420662000897 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 420662000898 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 420662000899 putative active site [active] 420662000900 substrate binding site [chemical binding]; other site 420662000901 putative cosubstrate binding site; other site 420662000902 catalytic site [active] 420662000903 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 420662000904 substrate binding site [chemical binding]; other site 420662000905 M48 family peptidase; Provisional; Region: PRK03001 420662000906 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 420662000907 AzlC protein; Region: AzlC; pfam03591 420662000908 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 420662000909 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 420662000910 Phosphoglycerate kinase; Region: PGK; pfam00162 420662000911 substrate binding site [chemical binding]; other site 420662000912 hinge regions; other site 420662000913 ADP binding site [chemical binding]; other site 420662000914 catalytic site [active] 420662000915 pyruvate kinase; Provisional; Region: PRK05826 420662000916 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 420662000917 domain interfaces; other site 420662000918 active site 420662000919 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 420662000920 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 420662000921 intersubunit interface [polypeptide binding]; other site 420662000922 active site 420662000923 zinc binding site [ion binding]; other site 420662000924 Na+ binding site [ion binding]; other site 420662000925 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 420662000926 active site 420662000927 ATP binding site [chemical binding]; other site 420662000928 substrate binding site [chemical binding]; other site 420662000929 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 420662000930 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 420662000931 AIR carboxylase; Region: AIRC; cl00310 420662000932 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 420662000933 ATP-grasp domain; Region: ATP-grasp; pfam02222 420662000934 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 420662000935 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 420662000936 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 420662000937 active site 420662000938 catalytic triad [active] 420662000939 oxyanion hole [active] 420662000940 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 420662000941 active site 420662000942 catalytic triad [active] 420662000943 oxyanion hole [active] 420662000944 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 420662000945 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 420662000946 Glycoprotease family; Region: Peptidase_M22; pfam00814 420662000947 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 420662000948 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662000949 Coenzyme A binding pocket [chemical binding]; other site 420662000950 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 420662000951 Fe-S cluster binding site [ion binding]; other site 420662000952 active site 420662000953 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 420662000954 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 420662000955 putative active site [active] 420662000956 heme pocket [chemical binding]; other site 420662000957 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 420662000958 putative active site [active] 420662000959 heme pocket [chemical binding]; other site 420662000960 PAS domain; Region: PAS_9; pfam13426 420662000961 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 420662000962 putative active site [active] 420662000963 heme pocket [chemical binding]; other site 420662000964 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662000965 metal binding site [ion binding]; metal-binding site 420662000966 active site 420662000967 I-site; other site 420662000968 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 420662000969 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 420662000970 oligomer interface [polypeptide binding]; other site 420662000971 metal binding site [ion binding]; metal-binding site 420662000972 metal binding site [ion binding]; metal-binding site 420662000973 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 420662000974 putative Cl binding site [ion binding]; other site 420662000975 aspartate ring; other site 420662000976 basic sphincter; other site 420662000977 hydrophobic gate; other site 420662000978 periplasmic entrance; other site 420662000979 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 420662000980 dimer interface [polypeptide binding]; other site 420662000981 active site 420662000982 aspartate-rich active site metal binding site; other site 420662000983 allosteric magnesium binding site [ion binding]; other site 420662000984 Schiff base residues; other site 420662000985 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 420662000986 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 420662000987 dimer interface [polypeptide binding]; other site 420662000988 [2Fe-2S] cluster binding site [ion binding]; other site 420662000989 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 420662000990 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 420662000991 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 420662000992 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 420662000993 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 420662000994 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 420662000995 homodimer interface [polypeptide binding]; other site 420662000996 substrate-cofactor binding pocket; other site 420662000997 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662000998 catalytic residue [active] 420662000999 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 420662001000 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 420662001001 Walker A/P-loop; other site 420662001002 ATP binding site [chemical binding]; other site 420662001003 Q-loop/lid; other site 420662001004 ABC transporter signature motif; other site 420662001005 Walker B; other site 420662001006 D-loop; other site 420662001007 H-loop/switch region; other site 420662001008 lipoate-protein ligase B; Provisional; Region: PRK14346 420662001009 lipoyl synthase; Provisional; Region: PRK05481 420662001010 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 420662001011 FeS/SAM binding site; other site 420662001012 HPP family; Region: HPP; pfam04982 420662001013 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; cl15354 420662001014 FOG: CBS domain [General function prediction only]; Region: COG0517 420662001015 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 420662001016 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 420662001017 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662001018 catalytic residues [active] 420662001019 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 420662001020 sensory histidine kinase CreC; Provisional; Region: PRK11100 420662001021 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 420662001022 CoA-transferase family III; Region: CoA_transf_3; pfam02515 420662001023 PTS_IIA, PTS system, mannose/sorbose 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 family...; Region: PTS_IIA_man; cl00025 420662001024 active pocket/dimerization site; other site 420662001025 active site 420662001026 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 420662001027 dimerization domain swap beta strand [polypeptide binding]; other site 420662001028 regulatory protein interface [polypeptide binding]; other site 420662001029 active site 420662001030 regulatory phosphorylation site [posttranslational modification]; other site 420662001031 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 420662001032 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 420662001033 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 420662001034 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 420662001035 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 420662001036 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 420662001037 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 420662001038 Walker A motif; other site 420662001039 ATP binding site [chemical binding]; other site 420662001040 Walker B motif; other site 420662001041 arginine finger; other site 420662001042 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 420662001043 Methyltransferase domain; Region: Methyltransf_31; pfam13847 420662001044 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 420662001045 S-adenosylmethionine binding site [chemical binding]; other site 420662001046 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 420662001047 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 420662001048 dimer interface [polypeptide binding]; other site 420662001049 active site 420662001050 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 420662001051 substrate binding site [chemical binding]; other site 420662001052 catalytic residue [active] 420662001053 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 420662001054 catalytic core [active] 420662001055 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 420662001056 substrate binding site [chemical binding]; other site 420662001057 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 420662001058 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 420662001059 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 420662001060 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 420662001061 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 420662001062 dimerization interface [polypeptide binding]; other site 420662001063 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662001064 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662001065 dimer interface [polypeptide binding]; other site 420662001066 putative CheW interface [polypeptide binding]; other site 420662001067 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 420662001068 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 420662001069 catalytic loop [active] 420662001070 iron binding site [ion binding]; other site 420662001071 4Fe-4S binding domain; Region: Fer4; pfam00037 420662001072 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 420662001073 [4Fe-4S] binding site [ion binding]; other site 420662001074 molybdopterin cofactor binding site; other site 420662001075 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 420662001076 molybdopterin cofactor binding site; other site 420662001077 NADH dehydrogenase subunit E; Validated; Region: PRK07539 420662001078 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 420662001079 putative dimer interface [polypeptide binding]; other site 420662001080 [2Fe-2S] cluster binding site [ion binding]; other site 420662001081 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 420662001082 SLBB domain; Region: SLBB; pfam10531 420662001083 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 420662001084 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 420662001085 PBP superfamily domain; Region: PBP_like; pfam12727 420662001086 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 420662001087 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662001088 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 420662001089 dimer interface [polypeptide binding]; other site 420662001090 Trp docking motif [polypeptide binding]; other site 420662001091 active site 420662001092 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662001093 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 420662001094 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_1; cd05974 420662001095 active site 420662001096 acyl-activating enzyme (AAE) consensus motif; other site 420662001097 putative CoA binding site [chemical binding]; other site 420662001098 AMP binding site [chemical binding]; other site 420662001099 AMP-binding domain protein; Validated; Region: PRK08315 420662001100 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662001101 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 420662001102 acyl-activating enzyme (AAE) consensus motif; other site 420662001103 putative AMP binding site [chemical binding]; other site 420662001104 putative active site [active] 420662001105 putative CoA binding site [chemical binding]; other site 420662001106 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662001107 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 420662001108 putative DNA binding site [nucleotide binding]; other site 420662001109 putative Zn2+ binding site [ion binding]; other site 420662001110 AsnC family; Region: AsnC_trans_reg; pfam01037 420662001111 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 420662001112 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 420662001113 dimer interface [polypeptide binding]; other site 420662001114 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 420662001115 active site 420662001116 Fe binding site [ion binding]; other site 420662001117 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 420662001118 cofactor binding site; other site 420662001119 metal binding site [ion binding]; metal-binding site 420662001120 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662001121 PGAP1-like protein; Region: PGAP1; pfam07819 420662001122 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 420662001123 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 420662001124 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 420662001125 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662001126 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 420662001127 acyl-activating enzyme (AAE) consensus motif; other site 420662001128 putative AMP binding site [chemical binding]; other site 420662001129 putative active site [active] 420662001130 putative CoA binding site [chemical binding]; other site 420662001131 OpgC protein; Region: OpgC_C; pfam10129 420662001132 Acyltransferase family; Region: Acyl_transf_3; pfam01757 420662001133 Members of the SGNH-hydrolase superfamily, 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 active site closely...; Region: SGNH_hydrolase_like_7; cd04502 420662001134 active site 420662001135 catalytic triad [active] 420662001136 oxyanion hole [active] 420662001137 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662001138 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 420662001139 active site 420662001140 phosphorylation site [posttranslational modification] 420662001141 intermolecular recognition site; other site 420662001142 dimerization interface [polypeptide binding]; other site 420662001143 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 420662001144 DNA binding residues [nucleotide binding] 420662001145 dimerization interface [polypeptide binding]; other site 420662001146 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; cl01054 420662001147 dimerization interface [polypeptide binding]; other site 420662001148 Histidine kinase; Region: HisKA_3; pfam07730 420662001149 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 420662001150 Mg2+ binding site [ion binding]; other site 420662001151 G-X-G motif; other site 420662001152 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662001153 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662001154 trimer interface [polypeptide binding]; other site 420662001155 eyelet of channel; other site 420662001156 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 420662001157 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 420662001158 phosphate binding site [ion binding]; other site 420662001159 Escherichia coli lactaldehyde dehydrogenase AldA-like; Region: ALDH_LactADH-AldA; cd07088 420662001160 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 420662001161 NAD binding site [chemical binding]; other site 420662001162 catalytic residues [active] 420662001163 substrate binding site [chemical binding]; other site 420662001164 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 420662001165 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662001166 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 420662001167 dimer interface [polypeptide binding]; other site 420662001168 Trp docking motif [polypeptide binding]; other site 420662001169 active site 420662001170 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 420662001171 iron-sulfur cluster [ion binding]; other site 420662001172 [2Fe-2S] cluster binding site [ion binding]; other site 420662001173 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662001174 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 420662001175 Walker A motif; other site 420662001176 ATP binding site [chemical binding]; other site 420662001177 Walker B motif; other site 420662001178 arginine finger; other site 420662001179 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662001180 Predicted membrane protein [Function unknown]; Region: COG2119 420662001181 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 420662001182 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 420662001183 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 420662001184 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 420662001185 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662001186 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 420662001187 dimerization interface [polypeptide binding]; other site 420662001188 Amino acid synthesis; Region: AA_synth; pfam06684 420662001189 EthD domain; Region: EthD; cl17553 420662001190 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 420662001191 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 420662001192 inhibitor-cofactor binding pocket; inhibition site 420662001193 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662001194 catalytic residue [active] 420662001195 Transposase; Region: DEDD_Tnp_IS110; pfam01548 420662001196 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 420662001197 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 420662001198 hypothetical protein; Provisional; Region: PRK10039 420662001199 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 420662001200 Transposase; Region: DEDD_Tnp_IS110; pfam01548 420662001201 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 420662001202 Transposase domain (DUF772); Region: DUF772; pfam05598 420662001203 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 420662001204 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662001205 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662001206 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 420662001207 Transposase; Region: DEDD_Tnp_IS110; pfam01548 420662001208 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 420662001209 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 420662001210 Electron transfer DM13; Region: DM13; pfam10517 420662001211 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662001212 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662001213 Beta-lactamase; Region: Beta-lactamase; pfam00144 420662001214 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 420662001215 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 420662001216 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662001217 acyl-activating enzyme (AAE) consensus motif; other site 420662001218 AMP binding site [chemical binding]; other site 420662001219 active site 420662001220 CoA binding site [chemical binding]; other site 420662001221 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662001222 GAF domain; Region: GAF; pfam01590 420662001223 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 420662001224 Walker A motif; other site 420662001225 ATP binding site [chemical binding]; other site 420662001226 Walker B motif; other site 420662001227 arginine finger; other site 420662001228 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662001229 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662001230 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662001231 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662001232 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 420662001233 C-terminal domain interface [polypeptide binding]; other site 420662001234 GSH binding site (G-site) [chemical binding]; other site 420662001235 dimer interface [polypeptide binding]; other site 420662001236 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 420662001237 substrate binding pocket (H-site) [chemical binding]; other site 420662001238 N-terminal domain interface [polypeptide binding]; other site 420662001239 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 420662001240 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 420662001241 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 420662001242 Uncharacterized conserved protein [Function unknown]; Region: COG3791 420662001243 NlpE N-terminal domain; Region: NlpE; pfam04170 420662001244 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 420662001245 Mechanosensitive ion channel; Region: MS_channel; pfam00924 420662001246 short chain dehydrogenase; Provisional; Region: PRK08278 420662001247 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662001248 NAD(P) binding site [chemical binding]; other site 420662001249 active site 420662001250 enoyl-CoA hydratase; Provisional; Region: PRK06688 420662001251 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 420662001252 substrate binding site [chemical binding]; other site 420662001253 oxyanion hole (OAH) forming residues; other site 420662001254 trimer interface [polypeptide binding]; other site 420662001255 Protein of unknown function (DUF1569); Region: DUF1569; pfam07606 420662001256 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 420662001257 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 420662001258 dimer interface [polypeptide binding]; other site 420662001259 active site 420662001260 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 420662001261 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662001262 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662001263 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 420662001264 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 420662001265 substrate binding site [chemical binding]; other site 420662001266 oxyanion hole (OAH) forming residues; other site 420662001267 trimer interface [polypeptide binding]; other site 420662001268 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 420662001269 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 420662001270 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 420662001271 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 420662001272 active site 420662001273 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 420662001274 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662001275 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662001276 FHA domain; Region: FHA; pfam00498 420662001277 phosphopeptide binding site; other site 420662001278 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 420662001279 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662001280 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 420662001281 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 420662001282 active site 420662001283 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 420662001284 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 420662001285 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 420662001286 Sulfate transporter family; Region: Sulfate_transp; pfam00916 420662001287 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 420662001288 conjugal transfer protein TraL; Provisional; Region: PRK13886 420662001289 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 420662001290 oligomerisation interface [polypeptide binding]; other site 420662001291 mobile loop; other site 420662001292 roof hairpin; other site 420662001293 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 420662001294 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 420662001295 ring oligomerisation interface [polypeptide binding]; other site 420662001296 ATP/Mg binding site [chemical binding]; other site 420662001297 stacking interactions; other site 420662001298 hinge regions; other site 420662001299 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 420662001300 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 420662001301 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 420662001302 active site 420662001303 nucleophile elbow; other site 420662001304 Surface antigen; Region: Bac_surface_Ag; pfam01103 420662001305 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 420662001306 G1 box; other site 420662001307 GTP/Mg2+ binding site [chemical binding]; other site 420662001308 Switch I region; other site 420662001309 G2 box; other site 420662001310 G3 box; other site 420662001311 Switch II region; other site 420662001312 G4 box; other site 420662001313 Cytochrome c553 [Energy production and conversion]; Region: COG2863 420662001314 Cytochrome c; Region: Cytochrom_C; cl11414 420662001315 ResB-like family; Region: ResB; pfam05140 420662001316 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 420662001317 ResB-like family; Region: ResB; pfam05140 420662001318 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 420662001319 TMAO/DMSO reductase; Reviewed; Region: PRK05363 420662001320 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 420662001321 Moco binding site; other site 420662001322 metal coordination site [ion binding]; other site 420662001323 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 420662001324 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 420662001325 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662001326 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 420662001327 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662001328 Walker A/P-loop; other site 420662001329 ATP binding site [chemical binding]; other site 420662001330 Q-loop/lid; other site 420662001331 ABC transporter signature motif; other site 420662001332 Walker B; other site 420662001333 D-loop; other site 420662001334 H-loop/switch region; other site 420662001335 YaeQ protein; Region: YaeQ; pfam07152 420662001336 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662001337 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662001338 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 420662001339 dimerization interface [polypeptide binding]; other site 420662001340 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 420662001341 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 420662001342 substrate binding pocket [chemical binding]; other site 420662001343 membrane-bound complex binding site; other site 420662001344 hinge residues; other site 420662001345 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 420662001346 dimer interface [polypeptide binding]; other site 420662001347 conserved gate region; other site 420662001348 putative PBP binding loops; other site 420662001349 ABC-ATPase subunit interface; other site 420662001350 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 420662001351 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 420662001352 dimer interface [polypeptide binding]; other site 420662001353 conserved gate region; other site 420662001354 putative PBP binding loops; other site 420662001355 ABC-ATPase subunit interface; other site 420662001356 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 420662001357 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 420662001358 Walker A/P-loop; other site 420662001359 ATP binding site [chemical binding]; other site 420662001360 Q-loop/lid; other site 420662001361 ABC transporter signature motif; other site 420662001362 Walker B; other site 420662001363 D-loop; other site 420662001364 H-loop/switch region; other site 420662001365 Domain of unknown function (DUF4394); Region: DUF4394; pfam14339 420662001366 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 420662001367 active site 420662001368 substrate binding pocket [chemical binding]; other site 420662001369 dimer interface [polypeptide binding]; other site 420662001370 LabA_like proteins; Region: LabA_like/DUF88; cl10034 420662001371 putative metal binding site [ion binding]; other site 420662001372 Uncharacterized conserved protein [Function unknown]; Region: COG1432 420662001373 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 420662001374 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 420662001375 dimer interface [polypeptide binding]; other site 420662001376 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662001377 catalytic residue [active] 420662001378 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 420662001379 putative substrate translocation pore; other site 420662001380 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 420662001381 putative hydrophobic ligand binding site [chemical binding]; other site 420662001382 cell division protein MraZ; Reviewed; Region: PRK00326 420662001383 MraZ protein; Region: MraZ; pfam02381 420662001384 MraZ protein; Region: MraZ; pfam02381 420662001385 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 420662001386 MraW methylase family; Region: Methyltransf_5; cl17771 420662001387 Cell division protein FtsL; Region: FtsL; pfam04999 420662001388 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 420662001389 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 420662001390 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 420662001391 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 420662001392 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662001393 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662001394 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 420662001395 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 420662001396 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662001397 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662001398 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 420662001399 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 420662001400 Mg++ binding site [ion binding]; other site 420662001401 putative catalytic motif [active] 420662001402 putative substrate binding site [chemical binding]; other site 420662001403 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 420662001404 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662001405 cell division protein FtsW; Region: ftsW; TIGR02614 420662001406 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 420662001407 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 420662001408 active site 420662001409 homodimer interface [polypeptide binding]; other site 420662001410 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 420662001411 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 420662001412 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662001413 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662001414 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 420662001415 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 420662001416 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662001417 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 420662001418 Cell division protein FtsQ; Region: FtsQ; pfam03799 420662001419 cell division protein FtsA; Region: ftsA; TIGR01174 420662001420 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 420662001421 nucleotide binding site [chemical binding]; other site 420662001422 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 420662001423 Cell division protein FtsA; Region: FtsA; pfam14450 420662001424 cell division protein FtsZ; Validated; Region: PRK09330 420662001425 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 420662001426 nucleotide binding site [chemical binding]; other site 420662001427 SulA interaction site; other site 420662001428 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 420662001429 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 420662001430 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 420662001431 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 420662001432 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 420662001433 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662001434 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662001435 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 420662001436 dimer interface [polypeptide binding]; other site 420662001437 Trp docking motif [polypeptide binding]; other site 420662001438 active site 420662001439 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662001440 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 420662001441 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 420662001442 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 420662001443 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 420662001444 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662001445 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 420662001446 dimer interface [polypeptide binding]; other site 420662001447 Trp docking motif [polypeptide binding]; other site 420662001448 active site 420662001449 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 420662001450 Histidine kinase; Region: HisKA_3; pfam07730 420662001451 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; cl00075 420662001452 Mg2+ binding site [ion binding]; other site 420662001453 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662001454 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 420662001455 active site 420662001456 phosphorylation site [posttranslational modification] 420662001457 intermolecular recognition site; other site 420662001458 dimerization interface [polypeptide binding]; other site 420662001459 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 420662001460 DNA binding residues [nucleotide binding] 420662001461 dimerization interface [polypeptide binding]; other site 420662001462 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662001463 GAF domain; Region: GAF; pfam01590 420662001464 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 420662001465 Walker A motif; other site 420662001466 ATP binding site [chemical binding]; other site 420662001467 Walker B motif; other site 420662001468 arginine finger; other site 420662001469 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 420662001470 DNA-binding interface [nucleotide binding]; DNA binding site 420662001471 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662001472 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 420662001473 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 420662001474 active site 420662001475 putative DNA-binding cleft [nucleotide binding]; other site 420662001476 dimer interface [polypeptide binding]; other site 420662001477 Cytidylyltransferase family; Region: CTP_transf_1; cl17467 420662001478 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 420662001479 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 420662001480 putative acyl-acceptor binding pocket; other site 420662001481 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 420662001482 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 420662001483 purine monophosphate binding site [chemical binding]; other site 420662001484 dimer interface [polypeptide binding]; other site 420662001485 putative catalytic residues [active] 420662001486 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 420662001487 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 420662001488 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 420662001489 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 420662001490 FMN binding site [chemical binding]; other site 420662001491 active site 420662001492 catalytic residues [active] 420662001493 substrate binding site [chemical binding]; other site 420662001494 Predicted membrane protein [Function unknown]; Region: COG1238 420662001495 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 420662001496 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 420662001497 short chain dehydrogenase; Provisional; Region: PRK07201 420662001498 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 420662001499 putative NAD(P) binding site [chemical binding]; other site 420662001500 active site 420662001501 putative substrate binding site [chemical binding]; other site 420662001502 classical (c) SDRs; Region: SDR_c; cd05233 420662001503 NAD(P) binding site [chemical binding]; other site 420662001504 active site 420662001505 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 420662001506 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 420662001507 Predicted metal-binding protein [General function prediction only]; Region: COG3019 420662001508 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 420662001509 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 420662001510 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 420662001511 Outer membrane efflux protein; Region: OEP; pfam02321 420662001512 Outer membrane efflux protein; Region: OEP; pfam02321 420662001513 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 420662001514 feedback inhibition sensing region; other site 420662001515 homohexameric interface [polypeptide binding]; other site 420662001516 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 420662001517 nucleotide binding site [chemical binding]; other site 420662001518 N-acetyl-L-glutamate binding site [chemical binding]; other site 420662001519 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 420662001520 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 420662001521 motif II; other site 420662001522 division inhibitor protein; Provisional; Region: slmA; PRK09480 420662001523 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662001524 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 420662001525 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 420662001526 Walker A motif; other site 420662001527 ATP binding site [chemical binding]; other site 420662001528 Walker B motif; other site 420662001529 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 420662001530 active site 420662001531 8-oxo-dGMP binding site [chemical binding]; other site 420662001532 nudix motif; other site 420662001533 metal binding site [ion binding]; metal-binding site 420662001534 Domain of unknown function (DUF329); Region: DUF329; pfam03884 420662001535 hypothetical protein; Provisional; Region: PRK05287 420662001536 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 420662001537 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 420662001538 CoA-binding site [chemical binding]; other site 420662001539 ATP-binding [chemical binding]; other site 420662001540 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 420662001541 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 420662001542 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 420662001543 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 420662001544 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 420662001545 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 420662001546 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 420662001547 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 420662001548 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 420662001549 Walker A motif; other site 420662001550 ATP binding site [chemical binding]; other site 420662001551 Walker B motif; other site 420662001552 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 420662001553 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 420662001554 substrate binding pocket [chemical binding]; other site 420662001555 chain length determination region; other site 420662001556 substrate-Mg2+ binding site; other site 420662001557 catalytic residues [active] 420662001558 aspartate-rich region 1; other site 420662001559 active site lid residues [active] 420662001560 aspartate-rich region 2; other site 420662001561 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 420662001562 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 420662001563 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 420662001564 GTPase CgtA; Reviewed; Region: obgE; PRK12299 420662001565 GTP1/OBG; Region: GTP1_OBG; pfam01018 420662001566 Obg GTPase; Region: Obg; cd01898 420662001567 G1 box; other site 420662001568 GTP/Mg2+ binding site [chemical binding]; other site 420662001569 Switch I region; other site 420662001570 G2 box; other site 420662001571 G3 box; other site 420662001572 Switch II region; other site 420662001573 G4 box; other site 420662001574 G5 box; other site 420662001575 gamma-glutamyl kinase; Provisional; Region: PRK05429 420662001576 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 420662001577 nucleotide binding site [chemical binding]; other site 420662001578 homotetrameric interface [polypeptide binding]; other site 420662001579 putative phosphate binding site [ion binding]; other site 420662001580 putative allosteric binding site; other site 420662001581 PUA domain; Region: PUA; pfam01472 420662001582 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662001583 EamA-like transporter family; Region: EamA; pfam00892 420662001584 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 420662001585 putative active site [active] 420662001586 Ap4A binding site [chemical binding]; other site 420662001587 nudix motif; other site 420662001588 putative metal binding site [ion binding]; other site 420662001589 prolyl-tRNA synthetase; Provisional; Region: PRK09194 420662001590 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 420662001591 dimer interface [polypeptide binding]; other site 420662001592 motif 1; other site 420662001593 active site 420662001594 motif 2; other site 420662001595 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 420662001596 putative deacylase active site [active] 420662001597 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 420662001598 active site 420662001599 motif 3; other site 420662001600 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 420662001601 anticodon binding site; other site 420662001602 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 420662001603 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 420662001604 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662001605 catalytic residue [active] 420662001606 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 420662001607 Flavoprotein; Region: Flavoprotein; pfam02441 420662001608 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 420662001609 putative GSH binding site [chemical binding]; other site 420662001610 catalytic residues [active] 420662001611 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 420662001612 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 420662001613 S-adenosylmethionine binding site [chemical binding]; other site 420662001614 peptide chain release factor 1; Validated; Region: prfA; PRK00591 420662001615 This domain is found in peptide chain release factors; Region: PCRF; smart00937 420662001616 RF-1 domain; Region: RF-1; pfam00472 420662001617 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 420662001618 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 420662001619 tRNA; other site 420662001620 putative tRNA binding site [nucleotide binding]; other site 420662001621 putative NADP binding site [chemical binding]; other site 420662001622 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 420662001623 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 420662001624 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 420662001625 FeS/SAM binding site; other site 420662001626 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 420662001627 active site 420662001628 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 420662001629 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 420662001630 inhibitor-cofactor binding pocket; inhibition site 420662001631 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662001632 catalytic residue [active] 420662001633 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 420662001634 AAA domain; Region: AAA_26; pfam13500 420662001635 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 420662001636 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 420662001637 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662001638 catalytic residue [active] 420662001639 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 420662001640 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 420662001641 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 420662001642 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 420662001643 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 420662001644 FeS/SAM binding site; other site 420662001645 TRAM domain; Region: TRAM; pfam01938 420662001646 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 420662001647 active site 420662001648 Zn binding site [ion binding]; other site 420662001649 multidrug resistance protein MdtN; Provisional; Region: PRK10476 420662001650 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 420662001651 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 420662001652 active site 420662001653 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 420662001654 Phage capsid family; Region: Phage_capsid; pfam05065 420662001655 AAA domain; Region: AAA_25; pfam13481 420662001656 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 420662001657 Walker A motif; other site 420662001658 ATP binding site [chemical binding]; other site 420662001659 Walker B motif; other site 420662001660 Sugar-specific transcriptional regulator TrmB; Region: TrmB; cl17775 420662001661 Phage integrase family; Region: Phage_integrase; pfam00589 420662001662 active site 420662001663 DNA binding site [nucleotide binding] 420662001664 Int/Topo IB signature motif; other site 420662001665 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 420662001666 Uncharacterized conserved protein [Function unknown]; Region: COG1565 420662001667 short chain dehydrogenase; Provisional; Region: PRK09134 420662001668 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662001669 NAD(P) binding site [chemical binding]; other site 420662001670 active site 420662001671 Dihydroneopterin aldolase; Region: FolB; smart00905 420662001672 active site 420662001673 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 420662001674 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 420662001675 Ligand Binding Site [chemical binding]; other site 420662001676 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 420662001677 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 420662001678 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 420662001679 Substrate binding site; other site 420662001680 Mg++ binding site; other site 420662001681 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 420662001682 active site 420662001683 substrate binding site [chemical binding]; other site 420662001684 CoA binding site [chemical binding]; other site 420662001685 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 420662001686 HSP70 interaction site [polypeptide binding]; other site 420662001687 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662001688 AsnC family; Region: AsnC_trans_reg; pfam01037 420662001689 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 420662001690 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 420662001691 glutaminase active site [active] 420662001692 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 420662001693 dimer interface [polypeptide binding]; other site 420662001694 active site 420662001695 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 420662001696 dimer interface [polypeptide binding]; other site 420662001697 active site 420662001698 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 420662001699 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662001700 catalytic residue [active] 420662001701 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 420662001702 putative rRNA binding site [nucleotide binding]; other site 420662001703 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 420662001704 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 420662001705 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 420662001706 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 420662001707 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 420662001708 FliG C-terminal domain; Region: FliG_C; pfam01706 420662001709 Flagellar assembly protein FliH; Region: FliH; pfam02108 420662001710 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 420662001711 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 420662001712 Walker A motif/ATP binding site; other site 420662001713 Walker B motif; other site 420662001714 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 420662001715 Flagellar FliJ protein; Region: FliJ; pfam02050 420662001716 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 420662001717 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 420662001718 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 420662001719 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 420662001720 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 420662001721 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 420662001722 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 420662001723 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 420662001724 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 420662001725 Peptidase family M48; Region: Peptidase_M48; cl12018 420662001726 Uncharacterized conserved protein [Function unknown]; Region: COG3791 420662001727 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 420662001728 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 420662001729 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662001730 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 420662001731 active site 420662001732 phosphorylation site [posttranslational modification] 420662001733 intermolecular recognition site; other site 420662001734 dimerization interface [polypeptide binding]; other site 420662001735 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 420662001736 DNA binding residues [nucleotide binding] 420662001737 dimerization interface [polypeptide binding]; other site 420662001738 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 420662001739 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662001740 active site 420662001741 phosphorylation site [posttranslational modification] 420662001742 intermolecular recognition site; other site 420662001743 dimerization interface [polypeptide binding]; other site 420662001744 Histidine kinase; Region: HisKA_3; pfam07730 420662001745 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 420662001746 ATP binding site [chemical binding]; other site 420662001747 Mg2+ binding site [ion binding]; other site 420662001748 G-X-G motif; other site 420662001749 Response regulator receiver domain; Region: Response_reg; pfam00072 420662001750 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 420662001751 active site 420662001752 phosphorylation site [posttranslational modification] 420662001753 intermolecular recognition site; other site 420662001754 dimerization interface [polypeptide binding]; other site 420662001755 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 420662001756 putative binding surface; other site 420662001757 active site 420662001758 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 420662001759 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 420662001760 ATP binding site [chemical binding]; other site 420662001761 Mg2+ binding site [ion binding]; other site 420662001762 G-X-G motif; other site 420662001763 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 420662001764 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 420662001765 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 420662001766 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 420662001767 dimerization interface [polypeptide binding]; other site 420662001768 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662001769 dimer interface [polypeptide binding]; other site 420662001770 putative CheW interface [polypeptide binding]; other site 420662001771 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 420662001772 Pirin-related protein [General function prediction only]; Region: COG1741 420662001773 Pirin; Region: Pirin; pfam02678 420662001774 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 420662001775 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 420662001776 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 420662001777 MOSC domain; Region: MOSC; pfam03473 420662001778 AsmA family; Region: AsmA; pfam05170 420662001779 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 420662001780 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 420662001781 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 420662001782 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 420662001783 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 420662001784 dimerization domain [polypeptide binding]; other site 420662001785 dimer interface [polypeptide binding]; other site 420662001786 catalytic residues [active] 420662001787 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 420662001788 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 420662001789 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 420662001790 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 420662001791 enoyl-CoA hydratase; Provisional; Region: PRK05862 420662001792 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 420662001793 substrate binding site [chemical binding]; other site 420662001794 oxyanion hole (OAH) forming residues; other site 420662001795 trimer interface [polypeptide binding]; other site 420662001796 Protein of unknown function (DUF779); Region: DUF779; pfam05610 420662001797 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 420662001798 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 420662001799 NAD(P) binding site [chemical binding]; other site 420662001800 catalytic residues [active] 420662001801 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 420662001802 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 420662001803 dimer interface [polypeptide binding]; other site 420662001804 putative anticodon binding site; other site 420662001805 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 420662001806 motif 1; other site 420662001807 active site 420662001808 motif 2; other site 420662001809 motif 3; other site 420662001810 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 420662001811 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 420662001812 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 420662001813 trimer interface [polypeptide binding]; other site 420662001814 active site 420662001815 substrate binding site [chemical binding]; other site 420662001816 CoA binding site [chemical binding]; other site 420662001817 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 420662001818 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 420662001819 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 420662001820 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 420662001821 Ligand binding site; other site 420662001822 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 420662001823 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 420662001824 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 420662001825 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 420662001826 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 420662001827 inhibitor-cofactor binding pocket; inhibition site 420662001828 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662001829 catalytic residue [active] 420662001830 Bacterial sugar transferase; Region: Bac_transf; pfam02397 420662001831 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 420662001832 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 420662001833 NAD(P) binding site [chemical binding]; other site 420662001834 homodimer interface [polypeptide binding]; other site 420662001835 substrate binding site [chemical binding]; other site 420662001836 active site 420662001837 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 420662001838 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662001839 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 420662001840 active site 420662001841 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 420662001842 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662001843 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 420662001844 active site 420662001845 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662001846 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 420662001847 active site 420662001848 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 420662001849 putative ADP-binding pocket [chemical binding]; other site 420662001850 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662001851 Methyltransferase domain; Region: Methyltransf_23; pfam13489 420662001852 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 420662001853 S-adenosylmethionine binding site [chemical binding]; other site 420662001854 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 420662001855 Methyltransferase domain; Region: Methyltransf_11; pfam08241 420662001856 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 420662001857 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 420662001858 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 420662001859 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 420662001860 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 420662001861 Walker A/P-loop; other site 420662001862 ATP binding site [chemical binding]; other site 420662001863 Q-loop/lid; other site 420662001864 ABC transporter signature motif; other site 420662001865 Walker B; other site 420662001866 D-loop; other site 420662001867 H-loop/switch region; other site 420662001868 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 420662001869 ABC-2 type transporter; Region: ABC2_membrane; cl17235 420662001870 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 420662001871 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 420662001872 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 420662001873 substrate binding site; other site 420662001874 tetramer interface; other site 420662001875 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 420662001876 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 420662001877 NADP binding site [chemical binding]; other site 420662001878 active site 420662001879 putative substrate binding site [chemical binding]; other site 420662001880 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 420662001881 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 420662001882 NAD binding site [chemical binding]; other site 420662001883 substrate binding site [chemical binding]; other site 420662001884 homodimer interface [polypeptide binding]; other site 420662001885 active site 420662001886 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 420662001887 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 420662001888 Substrate binding site; other site 420662001889 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 420662001890 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 420662001891 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 420662001892 Mg++ binding site [ion binding]; other site 420662001893 putative catalytic motif [active] 420662001894 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 420662001895 DEAD-like helicases superfamily; Region: DEXDc; smart00487 420662001896 ATP binding site [chemical binding]; other site 420662001897 Mg++ binding site [ion binding]; other site 420662001898 motif III; other site 420662001899 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 420662001900 nucleotide binding region [chemical binding]; other site 420662001901 ATP-binding site [chemical binding]; other site 420662001902 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 420662001903 active site 420662001904 homodimer interface [polypeptide binding]; other site 420662001905 SAM binding site [chemical binding]; other site 420662001906 Maf-like protein; Region: Maf; pfam02545 420662001907 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 420662001908 active site 420662001909 dimer interface [polypeptide binding]; other site 420662001910 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 420662001911 putative phosphate acyltransferase; Provisional; Region: PRK05331 420662001912 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 420662001913 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 420662001914 dimer interface [polypeptide binding]; other site 420662001915 active site 420662001916 CoA binding pocket [chemical binding]; other site 420662001917 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 420662001918 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 420662001919 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 420662001920 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 420662001921 NAD(P) binding site [chemical binding]; other site 420662001922 homotetramer interface [polypeptide binding]; other site 420662001923 homodimer interface [polypeptide binding]; other site 420662001924 active site 420662001925 acyl carrier protein; Provisional; Region: acpP; PRK00982 420662001926 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 420662001927 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 420662001928 dimer interface [polypeptide binding]; other site 420662001929 active site 420662001930 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 420662001931 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662001932 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 420662001933 DNA binding residues [nucleotide binding] 420662001934 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 420662001935 anti-sigma E factor; Provisional; Region: rseB; PRK09455 420662001936 MucB/RseB family; Region: MucB_RseB; pfam03888 420662001937 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 420662001938 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662001939 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 420662001940 GTP-binding protein LepA; Provisional; Region: PRK05433 420662001941 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 420662001942 G1 box; other site 420662001943 putative GEF interaction site [polypeptide binding]; other site 420662001944 GTP/Mg2+ binding site [chemical binding]; other site 420662001945 Switch I region; other site 420662001946 G2 box; other site 420662001947 G3 box; other site 420662001948 Switch II region; other site 420662001949 G4 box; other site 420662001950 G5 box; other site 420662001951 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 420662001952 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 420662001953 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 420662001954 signal peptidase I; Provisional; Region: PRK10861 420662001955 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 420662001956 Catalytic site [active] 420662001957 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 420662001958 ribonuclease III; Reviewed; Region: rnc; PRK00102 420662001959 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 420662001960 dimerization interface [polypeptide binding]; other site 420662001961 active site 420662001962 metal binding site [ion binding]; metal-binding site 420662001963 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 420662001964 GTPase Era; Reviewed; Region: era; PRK00089 420662001965 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 420662001966 G1 box; other site 420662001967 GTP/Mg2+ binding site [chemical binding]; other site 420662001968 Switch I region; other site 420662001969 G2 box; other site 420662001970 Switch II region; other site 420662001971 G3 box; other site 420662001972 G4 box; other site 420662001973 G5 box; other site 420662001974 KH domain; Region: KH_2; pfam07650 420662001975 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 420662001976 Recombination protein O N terminal; Region: RecO_N; pfam11967 420662001977 Recombination protein O C terminal; Region: RecO_C; pfam02565 420662001978 pyridoxine 5'-phosphate synthase; Provisional; Region: PRK05265 420662001979 active site 420662001980 hydrophilic channel; other site 420662001981 dimerization interface [polypeptide binding]; other site 420662001982 catalytic residues [active] 420662001983 active site lid [active] 420662001984 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 420662001985 beta-hexosaminidase; Provisional; Region: PRK05337 420662001986 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 420662001987 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 420662001988 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 420662001989 homodimer interface [polypeptide binding]; other site 420662001990 oligonucleotide binding site [chemical binding]; other site 420662001991 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 420662001992 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 420662001993 RNA binding surface [nucleotide binding]; other site 420662001994 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 420662001995 active site 420662001996 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 420662001997 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 420662001998 motif II; other site 420662001999 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 420662002000 iron-sulfur cluster [ion binding]; other site 420662002001 [2Fe-2S] cluster binding site [ion binding]; other site 420662002002 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 420662002003 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 420662002004 tandem repeat interface [polypeptide binding]; other site 420662002005 oligomer interface [polypeptide binding]; other site 420662002006 active site residues [active] 420662002007 PAS domain S-box; Region: sensory_box; TIGR00229 420662002008 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 420662002009 putative active site [active] 420662002010 heme pocket [chemical binding]; other site 420662002011 PAS fold; Region: PAS_4; pfam08448 420662002012 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 420662002013 putative active site [active] 420662002014 heme pocket [chemical binding]; other site 420662002015 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662002016 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662002017 metal binding site [ion binding]; metal-binding site 420662002018 active site 420662002019 I-site; other site 420662002020 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 420662002021 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 420662002022 BON domain; Region: BON; pfam04972 420662002023 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 420662002024 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 420662002025 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 420662002026 UreF; Region: UreF; pfam01730 420662002027 urease accessory protein UreE; Provisional; Region: ureE; PRK13263 420662002028 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 420662002029 dimer interface [polypeptide binding]; other site 420662002030 catalytic residues [active] 420662002031 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 420662002032 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 420662002033 urease subunit alpha; Reviewed; Region: ureC; PRK13207 420662002034 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 420662002035 subunit interactions [polypeptide binding]; other site 420662002036 active site 420662002037 flap region; other site 420662002038 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 420662002039 gamma-beta subunit interface [polypeptide binding]; other site 420662002040 alpha-beta subunit interface [polypeptide binding]; other site 420662002041 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 420662002042 alpha-gamma subunit interface [polypeptide binding]; other site 420662002043 beta-gamma subunit interface [polypeptide binding]; other site 420662002044 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 420662002045 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662002046 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 420662002047 dimer interface [polypeptide binding]; other site 420662002048 phosphorylation site [posttranslational modification] 420662002049 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 420662002050 ATP binding site [chemical binding]; other site 420662002051 Mg2+ binding site [ion binding]; other site 420662002052 G-X-G motif; other site 420662002053 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 420662002054 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 420662002055 active site 420662002056 phosphorylation site [posttranslational modification] 420662002057 intermolecular recognition site; other site 420662002058 dimerization interface [polypeptide binding]; other site 420662002059 Response regulator receiver domain; Region: Response_reg; pfam00072 420662002060 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 420662002061 active site 420662002062 phosphorylation site [posttranslational modification] 420662002063 intermolecular recognition site; other site 420662002064 dimerization interface [polypeptide binding]; other site 420662002065 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 420662002066 DNA binding residues [nucleotide binding] 420662002067 dimerization interface [polypeptide binding]; other site 420662002068 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 420662002069 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662002070 active site 420662002071 metal binding site [ion binding]; metal-binding site 420662002072 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 420662002073 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662002074 Isochorismatase family; Region: Isochorismatase; pfam00857 420662002075 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 420662002076 catalytic triad [active] 420662002077 conserved cis-peptide bond; other site 420662002078 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 420662002079 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662002080 active site 420662002081 Predicted acetyltransferase [General function prediction only]; Region: COG3393 420662002082 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 420662002083 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 420662002084 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 420662002085 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 420662002086 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 420662002087 N-terminal plug; other site 420662002088 ligand-binding site [chemical binding]; other site 420662002089 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 420662002090 DJ-1 family protein; Region: not_thiJ; TIGR01383 420662002091 conserved cys residue [active] 420662002092 Protein of unknown function (DUF461); Region: DUF461; pfam04314 420662002093 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 420662002094 putative hydrophobic ligand binding site [chemical binding]; other site 420662002095 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 420662002096 integron integrase; Region: integrase_gron; TIGR02249 420662002097 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 420662002098 Int/Topo IB signature motif; other site 420662002099 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662002100 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 420662002101 putative ligand binding site [chemical binding]; other site 420662002102 Flagellar hook-length control protein FliK; Region: Flg_hook; cl17777 420662002103 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 420662002104 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662002105 TM-ABC transporter signature motif; other site 420662002106 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 420662002107 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 420662002108 TM-ABC transporter signature motif; other site 420662002109 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 420662002110 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662002111 Walker A/P-loop; other site 420662002112 ATP binding site [chemical binding]; other site 420662002113 Q-loop/lid; other site 420662002114 ABC transporter signature motif; other site 420662002115 Walker B; other site 420662002116 D-loop; other site 420662002117 H-loop/switch region; other site 420662002118 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 420662002119 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662002120 Walker A/P-loop; other site 420662002121 ATP binding site [chemical binding]; other site 420662002122 Q-loop/lid; other site 420662002123 ABC transporter signature motif; other site 420662002124 Walker B; other site 420662002125 D-loop; other site 420662002126 H-loop/switch region; other site 420662002127 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662002128 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662002129 metal binding site [ion binding]; metal-binding site 420662002130 active site 420662002131 I-site; other site 420662002132 DNA photolyase; Region: DNA_photolyase; pfam00875 420662002133 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 420662002134 hypothetical protein; Validated; Region: PRK00228 420662002135 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 420662002136 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662002137 active site 420662002138 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 420662002139 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 420662002140 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 420662002141 dihydroorotase; Provisional; Region: PRK07627 420662002142 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 420662002143 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 420662002144 active site 420662002145 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 420662002146 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 420662002147 putative acyl-acceptor binding pocket; other site 420662002148 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 420662002149 catalytic core [active] 420662002150 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 420662002151 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 420662002152 active site residue [active] 420662002153 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 420662002154 GSH binding site [chemical binding]; other site 420662002155 catalytic residues [active] 420662002156 preprotein translocase subunit SecB; Validated; Region: PRK05751 420662002157 SecA binding site; other site 420662002158 Preprotein binding site; other site 420662002159 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 420662002160 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 420662002161 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 420662002162 sialate_O-acetylesterase_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: sialate_O-acetylesterase_like2; cd01828 420662002163 active site 420662002164 catalytic triad [active] 420662002165 oxyanion hole [active] 420662002166 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 420662002167 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 420662002168 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 420662002169 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 420662002170 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 420662002171 Ligand binding site; other site 420662002172 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 420662002173 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662002174 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 420662002175 active site 420662002176 catalytic residues [active] 420662002177 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662002178 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 420662002179 active site 420662002180 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 420662002181 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 420662002182 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 420662002183 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 420662002184 colanic acid exporter; Provisional; Region: PRK10459 420662002185 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 420662002186 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; cd02062 420662002187 FMN binding site [chemical binding]; other site 420662002188 dimer interface [polypeptide binding]; other site 420662002189 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 420662002190 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 420662002191 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 420662002192 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 420662002193 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 420662002194 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662002195 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 420662002196 active site 420662002197 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 420662002198 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 420662002199 chain length determinant protein EpsF; Region: EpsF; TIGR03017 420662002200 Chain length determinant protein; Region: Wzz; cl15801 420662002201 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 420662002202 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 420662002203 Bacterial sugar transferase; Region: Bac_transf; pfam02397 420662002204 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662002205 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 420662002206 UreD urease accessory protein; Region: UreD; pfam01774 420662002207 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 420662002208 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 420662002209 putative catalytic residue [active] 420662002210 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 420662002211 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662002212 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 420662002213 dimerization interface [polypeptide binding]; other site 420662002214 substrate binding pocket [chemical binding]; other site 420662002215 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 420662002216 Cupin domain; Region: Cupin_2; cl17218 420662002217 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 420662002218 PAS domain S-box; Region: sensory_box; TIGR00229 420662002219 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 420662002220 putative active site [active] 420662002221 heme pocket [chemical binding]; other site 420662002222 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 420662002223 PAS fold; Region: PAS_3; pfam08447 420662002224 putative active site [active] 420662002225 heme pocket [chemical binding]; other site 420662002226 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 420662002227 dimer interface [polypeptide binding]; other site 420662002228 phosphorylation site [posttranslational modification] 420662002229 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 420662002230 ATP binding site [chemical binding]; other site 420662002231 Mg2+ binding site [ion binding]; other site 420662002232 G-X-G motif; other site 420662002233 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 420662002234 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662002235 dimer interface [polypeptide binding]; other site 420662002236 putative CheW interface [polypeptide binding]; other site 420662002237 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 420662002238 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662002239 DNA-binding site [nucleotide binding]; DNA binding site 420662002240 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 420662002241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662002242 homodimer interface [polypeptide binding]; other site 420662002243 catalytic residue [active] 420662002244 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 420662002245 Cytochrome c; Region: Cytochrom_C; cl11414 420662002246 Cytochrome c; Region: Cytochrom_C; cl11414 420662002247 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 420662002248 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 420662002249 Cytochrome c; Region: Cytochrom_C; pfam00034 420662002250 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 420662002251 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 420662002252 putative active site [active] 420662002253 metal binding site [ion binding]; metal-binding site 420662002254 Beta-lactamase; Region: Beta-lactamase; pfam00144 420662002255 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 420662002256 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 420662002257 Metallo-dependent hydrolases, subgroup A 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_A; cd01299 420662002258 active site 420662002259 Hemerythrin-like domain of FBXL5-like proteins; Region: Hr_FBXL5; cd12109 420662002260 Fe binding site [ion binding]; other site 420662002261 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 420662002262 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662002263 DNA binding residues [nucleotide binding] 420662002264 dimerization interface [polypeptide binding]; other site 420662002265 Isochorismatase family; Region: Isochorismatase; pfam00857 420662002266 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 420662002267 catalytic triad [active] 420662002268 conserved cis-peptide bond; other site 420662002269 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 420662002270 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662002271 Walker A/P-loop; other site 420662002272 ATP binding site [chemical binding]; other site 420662002273 Q-loop/lid; other site 420662002274 ABC transporter signature motif; other site 420662002275 Walker B; other site 420662002276 D-loop; other site 420662002277 H-loop/switch region; other site 420662002278 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 420662002279 Isochorismatase family; Region: Isochorismatase; pfam00857 420662002280 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 420662002281 catalytic triad [active] 420662002282 conserved cis-peptide bond; other site 420662002283 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 420662002284 TM-ABC transporter signature motif; other site 420662002285 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 420662002286 TM-ABC transporter signature motif; other site 420662002287 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 420662002288 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 420662002289 putative ligand binding site [chemical binding]; other site 420662002290 Transcriptional regulators [Transcription]; Region: FadR; COG2186 420662002291 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662002292 DNA-binding site [nucleotide binding]; DNA binding site 420662002293 FCD domain; Region: FCD; pfam07729 420662002294 Protein of unknown function (DUF3225); Region: DUF3225; pfam11533 420662002295 amidase; Provisional; Region: PRK09201 420662002296 Amidase; Region: Amidase; cl11426 420662002297 allophanate hydrolase; Provisional; Region: PRK08186 420662002298 Amidase; Region: Amidase; cl11426 420662002299 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 420662002300 nucleoside/Zn binding site; other site 420662002301 dimer interface [polypeptide binding]; other site 420662002302 catalytic motif [active] 420662002303 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 420662002304 M20 Zn-peptidases include exopeptidases; Region: M20_like; cd02697 420662002305 putative metal binding site [ion binding]; other site 420662002306 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional; Region: PRK13590 420662002307 OHCU decarboxylase; Region: OHCU_decarbox; pfam09349 420662002308 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 420662002309 active site 420662002310 metal binding site [ion binding]; metal-binding site 420662002311 dimer interface [polypeptide binding]; other site 420662002312 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 420662002313 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 420662002314 active site 420662002315 catalytic site [active] 420662002316 tetramer interface [polypeptide binding]; other site 420662002317 Transcriptional regulators [Transcription]; Region: FadR; COG2186 420662002318 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662002319 DNA-binding site [nucleotide binding]; DNA binding site 420662002320 FCD domain; Region: FCD; pfam07729 420662002321 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 420662002322 active site 420662002323 homotetramer interface [polypeptide binding]; other site 420662002324 Predicted membrane protein [Function unknown]; Region: COG3748 420662002325 Protein of unknown function (DUF989); Region: DUF989; pfam06181 420662002326 Cytochrome c; Region: Cytochrom_C; pfam00034 420662002327 xanthine permease; Region: pbuX; TIGR03173 420662002328 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 420662002329 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 420662002330 active site 420662002331 putative substrate binding pocket [chemical binding]; other site 420662002332 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 420662002333 oligomerization interface [polypeptide binding]; other site 420662002334 active site 420662002335 metal binding site [ion binding]; metal-binding site 420662002336 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 420662002337 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 420662002338 non-specific DNA binding site [nucleotide binding]; other site 420662002339 salt bridge; other site 420662002340 sequence-specific DNA binding site [nucleotide binding]; other site 420662002341 Transcriptional regulators [Transcription]; Region: GntR; COG1802 420662002342 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662002343 DNA-binding site [nucleotide binding]; DNA binding site 420662002344 FCD domain; Region: FCD; pfam07729 420662002345 Acyl transferase domain; Region: Acyl_transf_1; cl08282 420662002346 triphosphoribosyl-dephospho-CoA synthase MdcB; Region: malonate_mdcB; TIGR03132 420662002347 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 420662002348 malonate decarboxylase holo-[acyl-carrier-protein] synthase; Region: malonate_mdcG; TIGR03135 420662002349 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 420662002350 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 420662002351 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 420662002352 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 420662002353 Coenzyme A transferase; Region: CoA_trans; cl17247 420662002354 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662002355 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK13027 420662002356 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 420662002357 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 420662002358 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 420662002359 XdhC Rossmann domain; Region: XdhC_C; pfam13478 420662002360 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 420662002361 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 420662002362 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 420662002363 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 420662002364 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 420662002365 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 420662002366 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662002367 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662002368 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 420662002369 dimerization interface [polypeptide binding]; other site 420662002370 guanine deaminase; Provisional; Region: PRK09228 420662002371 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 420662002372 active site 420662002373 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 420662002374 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 420662002375 Walker A/P-loop; other site 420662002376 ATP binding site [chemical binding]; other site 420662002377 Q-loop/lid; other site 420662002378 ABC transporter signature motif; other site 420662002379 Walker B; other site 420662002380 D-loop; other site 420662002381 H-loop/switch region; other site 420662002382 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 420662002383 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662002384 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 420662002385 TM-ABC transporter signature motif; other site 420662002386 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662002387 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 420662002388 TM-ABC transporter signature motif; other site 420662002389 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 420662002390 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 420662002391 putative ligand binding site [chemical binding]; other site 420662002392 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662002393 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 420662002394 [2Fe-2S] cluster binding site [ion binding]; other site 420662002395 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662002396 hydrophobic ligand binding site; other site 420662002397 Frag1/DRAM/Sfk1 family; Region: Frag1; pfam10277 420662002398 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 420662002399 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 420662002400 active site 420662002401 purine riboside binding site [chemical binding]; other site 420662002402 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 420662002403 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 420662002404 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 420662002405 active site 420662002406 phosphorylation site [posttranslational modification] 420662002407 intermolecular recognition site; other site 420662002408 dimerization interface [polypeptide binding]; other site 420662002409 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 420662002410 DNA binding residues [nucleotide binding] 420662002411 dimerization interface [polypeptide binding]; other site 420662002412 PAS domain S-box; Region: sensory_box; TIGR00229 420662002413 PAS domain; Region: PAS; smart00091 420662002414 putative active site [active] 420662002415 heme pocket [chemical binding]; other site 420662002416 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662002417 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 420662002418 dimer interface [polypeptide binding]; other site 420662002419 phosphorylation site [posttranslational modification] 420662002420 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 420662002421 ATP binding site [chemical binding]; other site 420662002422 Mg2+ binding site [ion binding]; other site 420662002423 G-X-G motif; other site 420662002424 Response regulator receiver domain; Region: Response_reg; pfam00072 420662002425 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 420662002426 active site 420662002427 phosphorylation site [posttranslational modification] 420662002428 intermolecular recognition site; other site 420662002429 dimerization interface [polypeptide binding]; other site 420662002430 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 420662002431 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 420662002432 putative active site [active] 420662002433 heme pocket [chemical binding]; other site 420662002434 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 420662002435 dimer interface [polypeptide binding]; other site 420662002436 phosphorylation site [posttranslational modification] 420662002437 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 420662002438 ATP binding site [chemical binding]; other site 420662002439 Mg2+ binding site [ion binding]; other site 420662002440 G-X-G motif; other site 420662002441 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662002442 dinuclear metal binding motif [ion binding]; other site 420662002443 Toluene-4-monooxygenase system protein B (TmoB); Region: TmoB; pfam06234 420662002444 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 420662002445 [2Fe-2S] cluster binding site [ion binding]; other site 420662002446 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 420662002447 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 420662002448 dimerization interface [polypeptide binding]; other site 420662002449 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662002450 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 420662002451 catalytic loop [active] 420662002452 iron binding site [ion binding]; other site 420662002453 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 420662002454 FAD binding pocket [chemical binding]; other site 420662002455 FAD binding motif [chemical binding]; other site 420662002456 phosphate binding motif [ion binding]; other site 420662002457 beta-alpha-beta structure motif; other site 420662002458 NAD binding pocket [chemical binding]; other site 420662002459 Formaldehyde dehydrogenases; Region: FDH_like; cd05278 420662002460 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 420662002461 catalytic Zn binding site [ion binding]; other site 420662002462 NAD(P) binding site [chemical binding]; other site 420662002463 structural Zn binding site [ion binding]; other site 420662002464 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 420662002465 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 420662002466 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 420662002467 dimerization interface [polypeptide binding]; other site 420662002468 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662002469 dimer interface [polypeptide binding]; other site 420662002470 putative CheW interface [polypeptide binding]; other site 420662002471 Protein of unknown function (DUF1330); Region: DUF1330; pfam07045 420662002472 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662002473 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662002474 Bacterial transcriptional repressor; Region: TetR; pfam13972 420662002475 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 420662002476 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 420662002477 Walker A/P-loop; other site 420662002478 ATP binding site [chemical binding]; other site 420662002479 Q-loop/lid; other site 420662002480 ABC transporter signature motif; other site 420662002481 Walker B; other site 420662002482 D-loop; other site 420662002483 H-loop/switch region; other site 420662002484 ABC-2 type transporter; Region: ABC2_membrane; cl17235 420662002485 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 420662002486 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 420662002487 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 420662002488 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 420662002489 hinge; other site 420662002490 active site 420662002491 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 420662002492 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 420662002493 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 420662002494 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 420662002495 NAD binding site [chemical binding]; other site 420662002496 dimerization interface [polypeptide binding]; other site 420662002497 product binding site; other site 420662002498 substrate binding site [chemical binding]; other site 420662002499 zinc binding site [ion binding]; other site 420662002500 catalytic residues [active] 420662002501 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 420662002502 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 420662002503 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662002504 homodimer interface [polypeptide binding]; other site 420662002505 catalytic residue [active] 420662002506 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 420662002507 putative active site pocket [active] 420662002508 4-fold oligomerization interface [polypeptide binding]; other site 420662002509 metal binding residues [ion binding]; metal-binding site 420662002510 3-fold/trimer interface [polypeptide binding]; other site 420662002511 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 420662002512 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 420662002513 putative active site [active] 420662002514 oxyanion strand; other site 420662002515 catalytic triad [active] 420662002516 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 420662002517 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 420662002518 catalytic residues [active] 420662002519 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 420662002520 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 420662002521 substrate binding site [chemical binding]; other site 420662002522 glutamase interaction surface [polypeptide binding]; other site 420662002523 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 420662002524 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 420662002525 metal binding site [ion binding]; metal-binding site 420662002526 Predicted membrane protein [Function unknown]; Region: COG3671 420662002527 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 420662002528 nucleotide binding site/active site [active] 420662002529 HIT family signature motif; other site 420662002530 catalytic residue [active] 420662002531 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 420662002532 twin arginine translocase protein A; Provisional; Region: tatA; PRK00442 420662002533 sec-independent translocase; Provisional; Region: tatB; PRK01919 420662002534 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 420662002535 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662002536 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 420662002537 protein binding site [polypeptide binding]; other site 420662002538 Uncharacterized conserved protein [Function unknown]; Region: COG0327 420662002539 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 420662002540 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 420662002541 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 420662002542 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 420662002543 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 420662002544 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 420662002545 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 420662002546 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 420662002547 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 420662002548 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 420662002549 [2Fe-2S] cluster binding site [ion binding]; other site 420662002550 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 420662002551 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 420662002552 Qi binding site; other site 420662002553 intrachain domain interface; other site 420662002554 interchain domain interface [polypeptide binding]; other site 420662002555 heme bH binding site [chemical binding]; other site 420662002556 heme bL binding site [chemical binding]; other site 420662002557 Qo binding site; other site 420662002558 Cytochrome b(C-terminus)/b6/petD: 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_C; cl00193 420662002559 interchain domain interface [polypeptide binding]; other site 420662002560 intrachain domain interface; other site 420662002561 Qi binding site; other site 420662002562 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 420662002563 Qo binding site; other site 420662002564 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 420662002565 stringent starvation protein A; Provisional; Region: sspA; PRK09481 420662002566 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 420662002567 C-terminal domain interface [polypeptide binding]; other site 420662002568 putative GSH binding site (G-site) [chemical binding]; other site 420662002569 dimer interface [polypeptide binding]; other site 420662002570 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 420662002571 dimer interface [polypeptide binding]; other site 420662002572 N-terminal domain interface [polypeptide binding]; other site 420662002573 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 420662002574 Transposase domain (DUF772); Region: DUF772; pfam05598 420662002575 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662002576 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662002577 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 420662002578 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 420662002579 4Fe-4S binding domain; Region: Fer4; pfam00037 420662002580 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 420662002581 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 420662002582 molybdopterin cofactor binding site; other site 420662002583 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 420662002584 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 420662002585 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal 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...; Region: MopB_CT_2; cd02783 420662002586 putative molybdopterin cofactor binding site; other site 420662002587 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 420662002588 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662002589 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 420662002590 putative dimerization interface [polypeptide binding]; other site 420662002591 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 420662002592 YciI-like protein; Reviewed; Region: PRK12863 420662002593 Cupin domain; Region: Cupin_2; cl17218 420662002594 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 420662002595 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 420662002596 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 420662002597 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 420662002598 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 420662002599 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662002600 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662002601 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662002602 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662002603 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662002604 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662002605 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 420662002606 putative effector binding pocket; other site 420662002607 putative dimerization interface [polypeptide binding]; other site 420662002608 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 420662002609 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 420662002610 putative substrate translocation pore; other site 420662002611 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662002612 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 420662002613 putative DNA binding site [nucleotide binding]; other site 420662002614 putative Zn2+ binding site [ion binding]; other site 420662002615 AsnC family; Region: AsnC_trans_reg; pfam01037 420662002616 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 420662002617 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 420662002618 dimer interface [polypeptide binding]; other site 420662002619 TPP-binding site [chemical binding]; other site 420662002620 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662002621 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 420662002622 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 420662002623 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662002624 Trp docking motif [polypeptide binding]; other site 420662002625 cytochrome domain interface [polypeptide binding]; other site 420662002626 active site 420662002627 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 420662002628 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662002629 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 420662002630 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 420662002631 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 420662002632 dimer interface [polypeptide binding]; other site 420662002633 active site 420662002634 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 420662002635 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662002636 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662002637 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662002638 enoyl-CoA hydratase; Provisional; Region: PRK05995 420662002639 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 420662002640 substrate binding site [chemical binding]; other site 420662002641 oxyanion hole (OAH) forming residues; other site 420662002642 trimer interface [polypeptide binding]; other site 420662002643 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662002644 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 420662002645 nucleophilic elbow; other site 420662002646 catalytic triad; other site 420662002647 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 420662002648 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662002649 NAD(P) binding site [chemical binding]; other site 420662002650 active site 420662002651 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662002652 short chain dehydrogenase; Validated; Region: PRK07069 420662002653 NAD(P) binding site [chemical binding]; other site 420662002654 active site 420662002655 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662002656 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662002657 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662002658 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662002659 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 420662002660 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662002661 substrate binding pocket [chemical binding]; other site 420662002662 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 420662002663 CoA-transferase family III; Region: CoA_transf_3; pfam02515 420662002664 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 420662002665 AAA domain; Region: AAA_30; pfam13604 420662002666 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 420662002667 DNA binding residues [nucleotide binding] 420662002668 dimerization interface [polypeptide binding]; other site 420662002669 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 420662002670 substrate binding site [chemical binding]; other site 420662002671 oxyanion hole (OAH) forming residues; other site 420662002672 trimer interface [polypeptide binding]; other site 420662002673 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 420662002674 acyl-CoA synthetase; Validated; Region: PRK08316 420662002675 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662002676 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 420662002677 acyl-activating enzyme (AAE) consensus motif; other site 420662002678 acyl-activating enzyme (AAE) consensus motif; other site 420662002679 putative AMP binding site [chemical binding]; other site 420662002680 putative active site [active] 420662002681 putative CoA binding site [chemical binding]; other site 420662002682 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662002683 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662002684 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 420662002685 hypothetical protein; Validated; Region: PRK07581 420662002686 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 420662002687 AAA domain; Region: AAA_30; pfam13604 420662002688 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 420662002689 DNA binding residues [nucleotide binding] 420662002690 dimerization interface [polypeptide binding]; other site 420662002691 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662002692 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662002693 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 420662002694 Zeta-crystallin with NADP-dependent quinone reductase activity (QOR); Region: zeta_crystallin; cd08253 420662002695 NAD(P) binding site [chemical binding]; other site 420662002696 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 420662002697 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662002698 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662002699 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 420662002700 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 420662002701 NADP binding site [chemical binding]; other site 420662002702 dimer interface [polypeptide binding]; other site 420662002703 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 420662002704 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 420662002705 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662002706 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 420662002707 B12 binding site [chemical binding]; other site 420662002708 cobalt ligand [ion binding]; other site 420662002709 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 420662002710 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 420662002711 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 420662002712 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 420662002713 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 420662002714 intersubunit interface [polypeptide binding]; other site 420662002715 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662002716 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 420662002717 Trp docking motif [polypeptide binding]; other site 420662002718 cytochrome domain interface [polypeptide binding]; other site 420662002719 active site 420662002720 Cytochrome c; Region: Cytochrom_C; pfam00034 420662002721 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 420662002722 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 420662002723 C-terminal domain interface [polypeptide binding]; other site 420662002724 GSH binding site (G-site) [chemical binding]; other site 420662002725 dimer interface [polypeptide binding]; other site 420662002726 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 420662002727 N-terminal domain interface [polypeptide binding]; other site 420662002728 putative dimer interface [polypeptide binding]; other site 420662002729 active site 420662002730 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662002731 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 420662002732 putative C-terminal domain interface [polypeptide binding]; other site 420662002733 putative GSH binding site (G-site) [chemical binding]; other site 420662002734 putative dimer interface [polypeptide binding]; other site 420662002735 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 420662002736 substrate binding pocket (H-site) [chemical binding]; other site 420662002737 N-terminal domain interface [polypeptide binding]; other site 420662002738 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 420662002739 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662002740 NAD(P) binding site [chemical binding]; other site 420662002741 active site 420662002742 DEAD-like helicases superfamily; Region: DEXDc2; smart00488 420662002743 DEAD_2; Region: DEAD_2; pfam06733 420662002744 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 420662002745 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 420662002746 bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a...; Region: bact_SoxC_Moco; cd02113 420662002747 Moco binding site; other site 420662002748 metal coordination site [ion binding]; other site 420662002749 dimerization interface [polypeptide binding]; other site 420662002750 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662002751 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662002752 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 420662002753 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 420662002754 dimer interface [polypeptide binding]; other site 420662002755 phosphorylation site [posttranslational modification] 420662002756 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 420662002757 ATP binding site [chemical binding]; other site 420662002758 Mg2+ binding site [ion binding]; other site 420662002759 G-X-G motif; other site 420662002760 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 420662002761 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 420662002762 active site 420662002763 phosphorylation site [posttranslational modification] 420662002764 intermolecular recognition site; other site 420662002765 dimerization interface [polypeptide binding]; other site 420662002766 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 420662002767 Walker A motif; other site 420662002768 ATP binding site [chemical binding]; other site 420662002769 Walker B motif; other site 420662002770 arginine finger; other site 420662002771 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662002772 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 420662002773 ligand binding site [chemical binding]; other site 420662002774 flexible hinge region; other site 420662002775 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 420662002776 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 420662002777 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 420662002778 Sulfate transporter family; Region: Sulfate_transp; pfam00916 420662002779 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 420662002780 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662002781 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 420662002782 [2Fe-2S] cluster binding site [ion binding]; other site 420662002783 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 420662002784 alpha subunit interface [polypeptide binding]; other site 420662002785 active site 420662002786 substrate binding site [chemical binding]; other site 420662002787 Fe binding site [ion binding]; other site 420662002788 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 420662002789 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 420662002790 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662002791 catalytic loop [active] 420662002792 iron binding site [ion binding]; other site 420662002793 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 420662002794 FAD binding pocket [chemical binding]; other site 420662002795 FAD binding motif [chemical binding]; other site 420662002796 phosphate binding motif [ion binding]; other site 420662002797 beta-alpha-beta structure motif; other site 420662002798 NAD binding pocket [chemical binding]; other site 420662002799 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 420662002800 [2Fe-2S] cluster binding site [ion binding]; other site 420662002801 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662002802 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 420662002803 ligand binding site [chemical binding]; other site 420662002804 flexible hinge region; other site 420662002805 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 420662002806 membrane-bound complex binding site; other site 420662002807 hinge residues; other site 420662002808 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662002809 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 420662002810 dimer interface [polypeptide binding]; other site 420662002811 conserved gate region; other site 420662002812 putative PBP binding loops; other site 420662002813 ABC-ATPase subunit interface; other site 420662002814 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 420662002815 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662002816 Walker A/P-loop; other site 420662002817 ATP binding site [chemical binding]; other site 420662002818 Q-loop/lid; other site 420662002819 ABC transporter signature motif; other site 420662002820 Walker B; other site 420662002821 D-loop; other site 420662002822 H-loop/switch region; other site 420662002823 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662002824 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 420662002825 dimer interface [polypeptide binding]; other site 420662002826 conserved gate region; other site 420662002827 putative PBP binding loops; other site 420662002828 ABC-ATPase subunit interface; other site 420662002829 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 420662002830 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662002831 Walker A/P-loop; other site 420662002832 ATP binding site [chemical binding]; other site 420662002833 Q-loop/lid; other site 420662002834 ABC transporter signature motif; other site 420662002835 Walker B; other site 420662002836 D-loop; other site 420662002837 H-loop/switch region; other site 420662002838 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 420662002839 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 420662002840 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662002841 Coenzyme A binding pocket [chemical binding]; other site 420662002842 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 420662002843 FMN binding site [chemical binding]; other site 420662002844 dimer interface [polypeptide binding]; other site 420662002845 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 420662002846 S-adenosylmethionine binding site [chemical binding]; other site 420662002847 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 420662002848 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662002849 dimer interface [polypeptide binding]; other site 420662002850 active site 420662002851 glutathione binding site [chemical binding]; other site 420662002852 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 420662002853 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 420662002854 PAS fold; Region: PAS_3; pfam08447 420662002855 putative active site [active] 420662002856 heme pocket [chemical binding]; other site 420662002857 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 420662002858 PAS fold; Region: PAS_3; pfam08447 420662002859 putative active site [active] 420662002860 heme pocket [chemical binding]; other site 420662002861 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662002862 putative CheW interface [polypeptide binding]; other site 420662002863 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 420662002864 D-arabinose dehydrogenase; Region: arabinose_DH_like; cd05284 420662002865 NAD binding site [chemical binding]; other site 420662002866 substrate binding site [chemical binding]; other site 420662002867 catalytic Zn binding site [ion binding]; other site 420662002868 structural Zn binding site [ion binding]; other site 420662002869 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 420662002870 putative hydrophobic ligand binding site [chemical binding]; other site 420662002871 protein interface [polypeptide binding]; other site 420662002872 gate; other site 420662002873 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 420662002874 putative hydrophobic ligand binding site [chemical binding]; other site 420662002875 protein interface [polypeptide binding]; other site 420662002876 gate; other site 420662002877 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 420662002878 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662002879 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662002880 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 420662002881 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662002882 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662002883 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 420662002884 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 420662002885 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 420662002886 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 420662002887 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 420662002888 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 420662002889 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 420662002890 structural tetrad; other site 420662002891 FOG: WD40 repeat [General function prediction only]; Region: COG2319 420662002892 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 420662002893 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 420662002894 dimerization interface [polypeptide binding]; other site 420662002895 putative path to active site cavity [active] 420662002896 diiron center [ion binding]; other site 420662002897 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662002898 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 420662002899 catalytic loop [active] 420662002900 iron binding site [ion binding]; other site 420662002901 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is...; Region: monooxygenase_like; cd06212 420662002902 FAD binding pocket [chemical binding]; other site 420662002903 FAD binding motif [chemical binding]; other site 420662002904 phosphate binding motif [ion binding]; other site 420662002905 beta-alpha-beta structure motif; other site 420662002906 NAD binding pocket [chemical binding]; other site 420662002907 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 420662002908 dimerization interface [polypeptide binding]; other site 420662002909 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 420662002910 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 420662002911 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 420662002912 ring oligomerisation interface [polypeptide binding]; other site 420662002913 ATP/Mg binding site [chemical binding]; other site 420662002914 stacking interactions; other site 420662002915 hinge regions; other site 420662002916 manganese transport protein MntH; Reviewed; Region: PRK00701 420662002917 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 420662002918 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662002919 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 420662002920 Walker A motif; other site 420662002921 ATP binding site [chemical binding]; other site 420662002922 Walker B motif; other site 420662002923 arginine finger; other site 420662002924 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662002925 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 420662002926 Predicted HD phosphohydrolase [General function prediction only]; Region: COG4341; cl17564 420662002927 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 420662002928 FAD binding domain; Region: FAD_binding_4; pfam01565 420662002929 FAD binding domain; Region: FAD_binding_4; pfam01565 420662002930 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 420662002931 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 420662002932 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 420662002933 Cysteine-rich domain; Region: CCG; pfam02754 420662002934 Cysteine-rich domain; Region: CCG; pfam02754 420662002935 Activator of aromatic catabolism; Region: XylR_N; pfam06505 420662002936 V4R domain; Region: V4R; pfam02830 420662002937 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 420662002938 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 420662002939 Walker A motif; other site 420662002940 ATP binding site [chemical binding]; other site 420662002941 Walker B motif; other site 420662002942 arginine finger; other site 420662002943 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662002944 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662002945 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 420662002946 iron-sulfur cluster [ion binding]; other site 420662002947 [2Fe-2S] cluster binding site [ion binding]; other site 420662002948 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662002949 hydrophobic ligand binding site; other site 420662002950 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 420662002951 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662002952 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662002953 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662002954 Transcriptional regulators [Transcription]; Region: PurR; COG1609 420662002955 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 420662002956 DNA binding site [nucleotide binding] 420662002957 domain linker motif; other site 420662002958 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 420662002959 putative ligand binding site [chemical binding]; other site 420662002960 putative dimerization interface [polypeptide binding]; other site 420662002961 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662002962 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 420662002963 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes; Region: D-glucarate_dehydratase; cd03323 420662002964 active site 420662002965 tetramer interface [polypeptide binding]; other site 420662002966 Transcriptional regulators [Transcription]; Region: FadR; COG2186 420662002967 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662002968 DNA-binding site [nucleotide binding]; DNA binding site 420662002969 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 420662002970 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662002971 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 420662002972 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 420662002973 putative ligand binding site [chemical binding]; other site 420662002974 NAD binding site [chemical binding]; other site 420662002975 catalytic site [active] 420662002976 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 420662002977 tartronate semialdehyde reductase; Provisional; Region: PRK15059 420662002978 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 420662002979 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 420662002980 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 420662002981 MOFRL family; Region: MOFRL; pfam05161 420662002982 ABC-2 type transporter; Region: ABC2_membrane; cl17235 420662002983 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 420662002984 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 420662002985 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 420662002986 Walker A/P-loop; other site 420662002987 ATP binding site [chemical binding]; other site 420662002988 Q-loop/lid; other site 420662002989 ABC transporter signature motif; other site 420662002990 Walker B; other site 420662002991 D-loop; other site 420662002992 H-loop/switch region; other site 420662002993 Ecdysteroid kinase; Region: EcKinase; cl17738 420662002994 Phosphotransferase enzyme family; Region: APH; pfam01636 420662002995 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 420662002996 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662002997 active site 420662002998 amidase; Provisional; Region: PRK07487 420662002999 Amidase; Region: Amidase; pfam01425 420662003000 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 420662003001 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 420662003002 putative trimer interface [polypeptide binding]; other site 420662003003 putative metal binding site [ion binding]; other site 420662003004 enoyl-CoA hydratase; Provisional; Region: PRK08140 420662003005 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 420662003006 substrate binding site [chemical binding]; other site 420662003007 oxyanion hole (OAH) forming residues; other site 420662003008 trimer interface [polypeptide binding]; other site 420662003009 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 420662003010 CoenzymeA binding site [chemical binding]; other site 420662003011 subunit interaction site [polypeptide binding]; other site 420662003012 PHB binding site; other site 420662003013 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662003014 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 420662003015 acyl-activating enzyme (AAE) consensus motif; other site 420662003016 AMP binding site [chemical binding]; other site 420662003017 active site 420662003018 CoA binding site [chemical binding]; other site 420662003019 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 420662003020 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 420662003021 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 420662003022 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 420662003023 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 420662003024 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 420662003025 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 420662003026 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 420662003027 FAD binding pocket [chemical binding]; other site 420662003028 FAD binding motif [chemical binding]; other site 420662003029 phosphate binding motif [ion binding]; other site 420662003030 beta-alpha-beta structure motif; other site 420662003031 NAD(p) ribose binding residues [chemical binding]; other site 420662003032 NAD binding pocket [chemical binding]; other site 420662003033 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 420662003034 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 420662003035 catalytic loop [active] 420662003036 iron binding site [ion binding]; other site 420662003037 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662003038 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662003039 Predicted amidohydrolase [General function prediction only]; Region: COG0388 420662003040 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 420662003041 putative active site [active] 420662003042 catalytic triad [active] 420662003043 putative dimer interface [polypeptide binding]; other site 420662003044 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 420662003045 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 420662003046 Major Facilitator Superfamily; Region: MFS_1; pfam07690 420662003047 putative substrate translocation pore; other site 420662003048 Hemerythrin-like domain; Region: Hr-like; cd12108 420662003049 Fe binding site [ion binding]; other site 420662003050 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 420662003051 MASE1; Region: MASE1; cl17823 420662003052 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662003053 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662003054 metal binding site [ion binding]; metal-binding site 420662003055 active site 420662003056 I-site; other site 420662003057 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 420662003058 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 420662003059 Walker A/P-loop; other site 420662003060 ATP binding site [chemical binding]; other site 420662003061 Q-loop/lid; other site 420662003062 ABC transporter signature motif; other site 420662003063 Walker B; other site 420662003064 D-loop; other site 420662003065 H-loop/switch region; other site 420662003066 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 420662003067 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662003068 iron-sulfur cluster [ion binding]; other site 420662003069 [2Fe-2S] cluster binding site [ion binding]; other site 420662003070 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662003071 hydrophobic ligand binding site; other site 420662003072 Activator of aromatic catabolism; Region: XylR_N; pfam06505 420662003073 The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons; Region: V4R; smart00989 420662003074 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 420662003075 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 420662003076 Walker A motif; other site 420662003077 ATP binding site [chemical binding]; other site 420662003078 Walker B motif; other site 420662003079 arginine finger; other site 420662003080 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 420662003081 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 420662003082 FMN-binding pocket [chemical binding]; other site 420662003083 flavin binding motif; other site 420662003084 phosphate binding motif [ion binding]; other site 420662003085 beta-alpha-beta structure motif; other site 420662003086 NAD binding pocket [chemical binding]; other site 420662003087 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 420662003088 catalytic loop [active] 420662003089 iron binding site [ion binding]; other site 420662003090 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 420662003091 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662003092 iron-sulfur cluster [ion binding]; other site 420662003093 [2Fe-2S] cluster binding site [ion binding]; other site 420662003094 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662003095 hydrophobic ligand binding site; other site 420662003096 Cupin; Region: Cupin_6; pfam12852 420662003097 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662003098 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 420662003099 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662003100 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 420662003101 progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; Region: 5beta-POR_like_SDR_a; cd08948 420662003102 NAD(P) binding site [chemical binding]; other site 420662003103 active site 420662003104 Protein of unknown function (DUF456); Region: DUF456; pfam04306 420662003105 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 420662003106 CoA binding domain; Region: CoA_binding_2; pfam13380 420662003107 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 420662003108 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 420662003109 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 420662003110 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662003111 Coenzyme A binding pocket [chemical binding]; other site 420662003112 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 420662003113 Transcriptional regulators [Transcription]; Region: GntR; COG1802 420662003114 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662003115 DNA-binding site [nucleotide binding]; DNA binding site 420662003116 FCD domain; Region: FCD; pfam07729 420662003117 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 420662003118 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 420662003119 active site 420662003120 substrate binding site [chemical binding]; other site 420662003121 coenzyme B12 binding site [chemical binding]; other site 420662003122 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 420662003123 B12 binding site [chemical binding]; other site 420662003124 cobalt ligand [ion binding]; other site 420662003125 membrane ATPase/protein kinase; Provisional; Region: PRK09435 420662003126 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 420662003127 Walker A; other site 420662003128 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 420662003129 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 420662003130 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 420662003131 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 420662003132 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 420662003133 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 420662003134 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 420662003135 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 420662003136 carboxyltransferase (CT) interaction site; other site 420662003137 biotinylation site [posttranslational modification]; other site 420662003138 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 420662003139 dimer interface [polypeptide binding]; other site 420662003140 substrate binding site [chemical binding]; other site 420662003141 metal binding site [ion binding]; metal-binding site 420662003142 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662003143 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662003144 metal binding site [ion binding]; metal-binding site 420662003145 active site 420662003146 I-site; other site 420662003147 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 420662003148 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 420662003149 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662003150 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 420662003151 Walker A/P-loop; other site 420662003152 ATP binding site [chemical binding]; other site 420662003153 Q-loop/lid; other site 420662003154 ABC transporter signature motif; other site 420662003155 Walker B; other site 420662003156 D-loop; other site 420662003157 H-loop/switch region; other site 420662003158 cyanophycin synthetase; Provisional; Region: PRK14016 420662003159 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662003160 cyanophycin synthetase; Provisional; Region: PRK14016 420662003161 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662003162 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662003163 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662003164 Protein of unknown function (DUF466); Region: DUF466; pfam04328 420662003165 carbon starvation protein A; Provisional; Region: PRK15015 420662003166 Carbon starvation protein CstA; Region: CstA; pfam02554 420662003167 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 420662003168 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662003169 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 420662003170 active site 420662003171 phosphorylation site [posttranslational modification] 420662003172 intermolecular recognition site; other site 420662003173 dimerization interface [polypeptide binding]; other site 420662003174 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 420662003175 DNA binding residues [nucleotide binding] 420662003176 dimerization interface [polypeptide binding]; other site 420662003177 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 420662003178 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 420662003179 Histidine kinase; Region: HisKA_3; pfam07730 420662003180 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 420662003181 ATP binding site [chemical binding]; other site 420662003182 Mg2+ binding site [ion binding]; other site 420662003183 G-X-G motif; other site 420662003184 Predicted dehydrogenase [General function prediction only]; Region: COG0579 420662003185 hydroxyglutarate oxidase; Provisional; Region: PRK11728 420662003186 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 420662003187 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 420662003188 Walker A motif; other site 420662003189 ATP binding site [chemical binding]; other site 420662003190 Walker B motif; other site 420662003191 arginine finger; other site 420662003192 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 420662003193 ATP binding site [chemical binding]; other site 420662003194 hypothetical protein; Provisional; Region: PRK06486 420662003195 active site 420662003196 intersubunit interface [polypeptide binding]; other site 420662003197 Zn2+ binding site [ion binding]; other site 420662003198 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662003199 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662003200 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 420662003201 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 420662003202 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 420662003203 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 420662003204 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 420662003205 S-adenosylmethionine binding site [chemical binding]; other site 420662003206 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 420662003207 Protein export membrane protein; Region: SecD_SecF; cl14618 420662003208 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662003209 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662003210 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662003211 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662003212 Protein Disulfide Isomerase (PDIb) family, redox inactive TRX-like domain b; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family...; Region: PDI_b_family; cd02981 420662003213 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 420662003214 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662003215 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662003216 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 420662003217 dimerization interface [polypeptide binding]; other site 420662003218 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662003219 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 420662003220 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 420662003221 Transposase domain (DUF772); Region: DUF772; pfam05598 420662003222 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662003223 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662003224 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 420662003225 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662003226 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 420662003227 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662003228 Transposase; Region: HTH_Tnp_1; pfam01527 420662003229 putative transposase OrfB; Reviewed; Region: PHA02517 420662003230 HTH-like domain; Region: HTH_21; pfam13276 420662003231 Integrase core domain; Region: rve; pfam00665 420662003232 Integrase core domain; Region: rve_3; pfam13683 420662003233 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 420662003234 Putative catalytic NodB homology domain of gellan lyase and similar proteins; Region: CE4_GLA_like_6s; cd10967 420662003235 putative active site [active] 420662003236 putative metal binding site [ion binding]; other site 420662003237 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 420662003238 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 420662003239 Bacterial sugar transferase; Region: Bac_transf; pfam02397 420662003240 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 420662003241 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 420662003242 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 420662003243 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 420662003244 Uncharacterized conserved protein [Function unknown]; Region: COG2928 420662003245 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 420662003246 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 420662003247 dimer interface [polypeptide binding]; other site 420662003248 anticodon binding site; other site 420662003249 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 420662003250 homodimer interface [polypeptide binding]; other site 420662003251 motif 1; other site 420662003252 active site 420662003253 motif 2; other site 420662003254 GAD domain; Region: GAD; pfam02938 420662003255 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 420662003256 motif 3; other site 420662003257 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_7; cd04664 420662003258 nudix motif; other site 420662003259 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 420662003260 putative catalytic site [active] 420662003261 putative metal binding site [ion binding]; other site 420662003262 putative phosphate binding site [ion binding]; other site 420662003263 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 420662003264 putative active site [active] 420662003265 catalytic site [active] 420662003266 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 420662003267 PLD-like domain; Region: PLDc_2; pfam13091 420662003268 putative active site [active] 420662003269 catalytic site [active] 420662003270 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 420662003271 active site 420662003272 Sensors of blue-light using FAD; Region: BLUF; smart01034 420662003273 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662003274 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 420662003275 N-terminal plug; other site 420662003276 ligand-binding site [chemical binding]; other site 420662003277 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 420662003278 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 420662003279 Uncharacterized conserved protein [Function unknown]; Region: COG3339 420662003280 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 420662003281 Catalytic site; other site 420662003282 Arginase family; Region: Arginase; cd09989 420662003283 agmatinase; Region: agmatinase; TIGR01230 420662003284 active site 420662003285 Mn binding site [ion binding]; other site 420662003286 oligomer interface [polypeptide binding]; other site 420662003287 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 420662003288 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 420662003289 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 420662003290 ATP binding site [chemical binding]; other site 420662003291 substrate interface [chemical binding]; other site 420662003292 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 420662003293 C-terminal peptidase (prc); Region: prc; TIGR00225 420662003294 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 420662003295 protein binding site [polypeptide binding]; other site 420662003296 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 420662003297 Catalytic dyad [active] 420662003298 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 420662003299 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 420662003300 Walker A/P-loop; other site 420662003301 ATP binding site [chemical binding]; other site 420662003302 Q-loop/lid; other site 420662003303 ABC transporter signature motif; other site 420662003304 Walker B; other site 420662003305 D-loop; other site 420662003306 H-loop/switch region; other site 420662003307 TOBE domain; Region: TOBE_2; pfam08402 420662003308 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 420662003309 integrase; Provisional; Region: PRK09692 420662003310 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 420662003311 active site 420662003312 Int/Topo IB signature motif; other site 420662003313 Family of unknown function (DUF490); Region: DUF490; pfam04357 420662003314 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 420662003315 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662003316 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662003317 Surface antigen; Region: Bac_surface_Ag; pfam01103 420662003318 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 420662003319 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 420662003320 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 420662003321 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 420662003322 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662003323 Walker A motif; other site 420662003324 ATP binding site [chemical binding]; other site 420662003325 Walker B motif; other site 420662003326 arginine finger; other site 420662003327 Cytochrome c; Region: Cytochrom_C; cl11414 420662003328 Cytochrome c; Region: Cytochrom_C; cl11414 420662003329 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 420662003330 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 420662003331 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662003332 Zn2+ binding site [ion binding]; other site 420662003333 Mg2+ binding site [ion binding]; other site 420662003334 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_2; cd08498 420662003335 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 420662003336 Predicted membrane protein [Function unknown]; Region: COG2860 420662003337 UPF0126 domain; Region: UPF0126; pfam03458 420662003338 UPF0126 domain; Region: UPF0126; pfam03458 420662003339 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 420662003340 enoyl-CoA hydratase; Provisional; Region: PRK06127 420662003341 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 420662003342 substrate binding site [chemical binding]; other site 420662003343 oxyanion hole (OAH) forming residues; other site 420662003344 trimer interface [polypeptide binding]; other site 420662003345 malonyl-CoA synthase; Validated; Region: PRK07514 420662003346 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 420662003347 acyl-activating enzyme (AAE) consensus motif; other site 420662003348 active site 420662003349 AMP binding site [chemical binding]; other site 420662003350 CoA binding site [chemical binding]; other site 420662003351 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 420662003352 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662003353 Coenzyme A binding pocket [chemical binding]; other site 420662003354 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 420662003355 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 420662003356 RimM N-terminal domain; Region: RimM; pfam01782 420662003357 PRC-barrel domain; Region: PRC; pfam05239 420662003358 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 420662003359 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 420662003360 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 420662003361 putative active site [active] 420662003362 putative CoA binding site [chemical binding]; other site 420662003363 nudix motif; other site 420662003364 metal binding site [ion binding]; metal-binding site 420662003365 CobD/Cbib protein; Region: CobD_Cbib; cl00561 420662003366 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 420662003367 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662003368 substrate binding pocket [chemical binding]; other site 420662003369 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 420662003370 argininosuccinate lyase; Provisional; Region: PRK00855 420662003371 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 420662003372 active sites [active] 420662003373 tetramer interface [polypeptide binding]; other site 420662003374 Histidine kinase; Region: His_kinase; pfam06580 420662003375 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 420662003376 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 420662003377 active site 420662003378 phosphorylation site [posttranslational modification] 420662003379 intermolecular recognition site; other site 420662003380 dimerization interface [polypeptide binding]; other site 420662003381 LytTr DNA-binding domain; Region: LytTR; smart00850 420662003382 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 420662003383 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 420662003384 Fatty acid desaturase; Region: FA_desaturase; pfam00487 420662003385 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 420662003386 Di-iron ligands [ion binding]; other site 420662003387 Transposase; Region: DDE_Tnp_ISL3; pfam01610 420662003388 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 420662003389 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 420662003390 thioredoxin reductase; Provisional; Region: PRK10262 420662003391 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662003392 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662003393 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662003394 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 420662003395 ligand binding site [chemical binding]; other site 420662003396 flexible hinge region; other site 420662003397 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 420662003398 putative switch regulator; other site 420662003399 non-specific DNA interactions [nucleotide binding]; other site 420662003400 DNA binding site [nucleotide binding] 420662003401 sequence specific DNA binding site [nucleotide binding]; other site 420662003402 putative cAMP binding site [chemical binding]; other site 420662003403 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 420662003404 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 420662003405 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 420662003406 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 420662003407 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 420662003408 recombination factor protein RarA; Reviewed; Region: PRK13342 420662003409 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 420662003410 Walker A motif; other site 420662003411 ATP binding site [chemical binding]; other site 420662003412 Walker B motif; other site 420662003413 arginine finger; other site 420662003414 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 420662003415 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662003416 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 420662003417 TM-ABC transporter signature motif; other site 420662003418 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 420662003419 TM-ABC transporter signature motif; other site 420662003420 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 420662003421 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662003422 Walker A/P-loop; other site 420662003423 ATP binding site [chemical binding]; other site 420662003424 Q-loop/lid; other site 420662003425 ABC transporter signature motif; other site 420662003426 Walker B; other site 420662003427 D-loop; other site 420662003428 H-loop/switch region; other site 420662003429 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 420662003430 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662003431 Walker A/P-loop; other site 420662003432 ATP binding site [chemical binding]; other site 420662003433 Q-loop/lid; other site 420662003434 ABC transporter signature motif; other site 420662003435 Walker B; other site 420662003436 D-loop; other site 420662003437 H-loop/switch region; other site 420662003438 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662003439 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 420662003440 catalytic loop [active] 420662003441 iron binding site [ion binding]; other site 420662003442 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 420662003443 FAD binding pocket [chemical binding]; other site 420662003444 FAD binding motif [chemical binding]; other site 420662003445 phosphate binding motif [ion binding]; other site 420662003446 beta-alpha-beta structure motif; other site 420662003447 NAD binding pocket [chemical binding]; other site 420662003448 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662003449 NADH(P)-binding; Region: NAD_binding_10; pfam13460 420662003450 NAD(P) binding site [chemical binding]; other site 420662003451 active site 420662003452 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 420662003453 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662003454 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 420662003455 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 420662003456 cysteine synthase B; Region: cysM; TIGR01138 420662003457 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 420662003458 dimer interface [polypeptide binding]; other site 420662003459 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662003460 catalytic residue [active] 420662003461 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; cl00447 420662003462 nudix motif; other site 420662003463 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 420662003464 CPxP motif; other site 420662003465 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 420662003466 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 420662003467 active site 420662003468 tetramer interface; other site 420662003469 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 420662003470 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 420662003471 NAD binding site [chemical binding]; other site 420662003472 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 420662003473 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 420662003474 active site 420662003475 HIGH motif; other site 420662003476 nucleotide binding site [chemical binding]; other site 420662003477 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 420662003478 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 420662003479 active site 420662003480 KMSKS motif; other site 420662003481 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 420662003482 tRNA binding surface [nucleotide binding]; other site 420662003483 anticodon binding site; other site 420662003484 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 420662003485 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 420662003486 Predicted membrane protein [Function unknown]; Region: COG3212 420662003487 Predicted membrane protein [Function unknown]; Region: COG3212 420662003488 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 420662003489 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662003490 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 420662003491 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 420662003492 catalytic triad [active] 420662003493 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 420662003494 Part of AAA domain; Region: AAA_19; pfam13245 420662003495 Family description; Region: UvrD_C_2; pfam13538 420662003496 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 420662003497 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 420662003498 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 420662003499 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 420662003500 putative active site [active] 420662003501 putative substrate binding site [chemical binding]; other site 420662003502 ATP binding site [chemical binding]; other site 420662003503 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 420662003504 DNA polymerase I; Provisional; Region: PRK05755 420662003505 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 420662003506 active site 420662003507 metal binding site 1 [ion binding]; metal-binding site 420662003508 putative 5' ssDNA interaction site; other site 420662003509 metal binding site 3; metal-binding site 420662003510 metal binding site 2 [ion binding]; metal-binding site 420662003511 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 420662003512 putative DNA binding site [nucleotide binding]; other site 420662003513 putative metal binding site [ion binding]; other site 420662003514 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 420662003515 active site 420662003516 catalytic site [active] 420662003517 substrate binding site [chemical binding]; other site 420662003518 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 420662003519 active site 420662003520 DNA binding site [nucleotide binding] 420662003521 catalytic site [active] 420662003522 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662003523 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 420662003524 dimer interface [polypeptide binding]; other site 420662003525 phosphorylation site [posttranslational modification] 420662003526 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 420662003527 ATP binding site [chemical binding]; other site 420662003528 Mg2+ binding site [ion binding]; other site 420662003529 G-X-G motif; other site 420662003530 Response regulator receiver domain; Region: Response_reg; pfam00072 420662003531 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 420662003532 active site 420662003533 phosphorylation site [posttranslational modification] 420662003534 intermolecular recognition site; other site 420662003535 dimerization interface [polypeptide binding]; other site 420662003536 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662003537 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 420662003538 active site 420662003539 phosphorylation site [posttranslational modification] 420662003540 intermolecular recognition site; other site 420662003541 dimerization interface [polypeptide binding]; other site 420662003542 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 420662003543 DNA binding residues [nucleotide binding] 420662003544 dimerization interface [polypeptide binding]; other site 420662003545 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 420662003546 putative active site [active] 420662003547 putative catalytic site [active] 420662003548 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 420662003549 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 420662003550 P-loop; other site 420662003551 Magnesium ion binding site [ion binding]; other site 420662003552 pantoate--beta-alanine ligase; Region: panC; TIGR00018 420662003553 Pantoate-beta-alanine ligase; Region: PanC; cd00560 420662003554 active site 420662003555 ATP-binding site [chemical binding]; other site 420662003556 pantoate-binding site; other site 420662003557 HXXH motif; other site 420662003558 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 420662003559 oligomerization interface [polypeptide binding]; other site 420662003560 active site 420662003561 metal binding site [ion binding]; metal-binding site 420662003562 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 420662003563 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 420662003564 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 420662003565 putative active site [active] 420662003566 putative metal binding residues [ion binding]; other site 420662003567 signature motif; other site 420662003568 putative triphosphate binding site [ion binding]; other site 420662003569 CHAD domain; Region: CHAD; pfam05235 420662003570 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 420662003571 putative transporter; Provisional; Region: PRK11660 420662003572 Sulfate transporter family; Region: Sulfate_transp; pfam00916 420662003573 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 420662003574 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 420662003575 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 420662003576 active site 420662003577 HIGH motif; other site 420662003578 KMSKS motif; other site 420662003579 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 420662003580 anticodon binding site; other site 420662003581 tRNA binding surface [nucleotide binding]; other site 420662003582 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 420662003583 dimer interface [polypeptide binding]; other site 420662003584 putative tRNA-binding site [nucleotide binding]; other site 420662003585 PAS domain S-box; Region: sensory_box; TIGR00229 420662003586 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 420662003587 putative active site [active] 420662003588 heme pocket [chemical binding]; other site 420662003589 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 420662003590 ATP binding site [chemical binding]; other site 420662003591 G-X-G motif; other site 420662003592 Domain of unknown function DUF59; Region: DUF59; pfam01883 420662003593 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 420662003594 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 420662003595 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 420662003596 4Fe-4S binding domain; Region: Fer4; pfam00037 420662003597 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 420662003598 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 420662003599 4Fe-4S binding domain; Region: Fer4; pfam00037 420662003600 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 420662003601 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 420662003602 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 420662003603 dimerization interface [polypeptide binding]; other site 420662003604 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 420662003605 dimer interface [polypeptide binding]; other site 420662003606 phosphorylation site [posttranslational modification] 420662003607 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 420662003608 ATP binding site [chemical binding]; other site 420662003609 Mg2+ binding site [ion binding]; other site 420662003610 G-X-G motif; other site 420662003611 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 420662003612 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 420662003613 active site 420662003614 phosphorylation site [posttranslational modification] 420662003615 intermolecular recognition site; other site 420662003616 dimerization interface [polypeptide binding]; other site 420662003617 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 420662003618 Walker A motif; other site 420662003619 ATP binding site [chemical binding]; other site 420662003620 Walker B motif; other site 420662003621 arginine finger; other site 420662003622 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662003623 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 420662003624 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 420662003625 [4Fe-4S] binding site [ion binding]; other site 420662003626 molybdopterin cofactor binding site; other site 420662003627 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 420662003628 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 420662003629 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 420662003630 molybdopterin cofactor binding site; other site 420662003631 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 420662003632 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 420662003633 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 420662003634 Domain of unknown function (DUF4399); Region: DUF4399; pfam14347 420662003635 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 420662003636 deoxycytidine triphosphate deaminase; Reviewed; Region: dcd; PRK00416 420662003637 Protein of unknown function (DUF4007); Region: DUF4007; pfam13182 420662003638 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 420662003639 Active Sites [active] 420662003640 Protein of unknown function DUF262; Region: DUF262; pfam03235 420662003641 Uncharacterized conserved protein [Function unknown]; Region: COG1479 420662003642 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 420662003643 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 420662003644 Methyltransferase domain; Region: Methyltransf_23; pfam13489 420662003645 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 420662003646 S-adenosylmethionine binding site [chemical binding]; other site 420662003647 DNA phosphorothioation-associated putative methyltransferase; Region: dnd_rel_methyl; TIGR04096 420662003648 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 420662003649 ParB-like nuclease domain; Region: ParB; smart00470 420662003650 RepB plasmid partitioning protein; Region: RepB; pfam07506 420662003651 ParB-like nuclease domain; Region: ParB; smart00470 420662003652 RepB plasmid partitioning protein; Region: RepB; pfam07506 420662003653 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 420662003654 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 420662003655 catalytic residues [active] 420662003656 catalytic nucleophile [active] 420662003657 Recombinase; Region: Recombinase; pfam07508 420662003658 HNH endonuclease; Region: HNH_2; pfam13391 420662003659 DnaB-like helicase C terminal domain; Region: DnaB_C; pfam03796 420662003660 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 420662003661 Walker A motif; other site 420662003662 ATP binding site [chemical binding]; other site 420662003663 Walker B motif; other site 420662003664 DNA binding loops [nucleotide binding] 420662003665 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 420662003666 non-specific DNA binding site [nucleotide binding]; other site 420662003667 salt bridge; other site 420662003668 sequence-specific DNA binding site [nucleotide binding]; other site 420662003669 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 420662003670 catalytic motif [active] 420662003671 Zn binding site [ion binding]; other site 420662003672 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 420662003673 active site 420662003674 Int/Topo IB signature motif; other site 420662003675 DNA binding site [nucleotide binding] 420662003676 Predicted metalloprotease [General function prediction only]; Region: COG2321 420662003677 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 420662003678 TPR repeat; Region: TPR_11; pfam13414 420662003679 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 420662003680 binding surface 420662003681 TPR motif; other site 420662003682 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 420662003683 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 420662003684 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 420662003685 catalytic residues [active] 420662003686 central insert; other site 420662003687 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 420662003688 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 420662003689 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 420662003690 CcmB protein; Region: CcmB; cl17444 420662003691 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 420662003692 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662003693 Walker A/P-loop; other site 420662003694 ATP binding site [chemical binding]; other site 420662003695 Q-loop/lid; other site 420662003696 ABC transporter signature motif; other site 420662003697 Walker B; other site 420662003698 D-loop; other site 420662003699 H-loop/switch region; other site 420662003700 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 420662003701 ApbE family; Region: ApbE; pfam02424 420662003702 translocation protein TolB; Provisional; Region: tolB; PRK05137 420662003703 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 420662003704 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 420662003705 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 420662003706 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662003707 catalytic residues [active] 420662003708 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 420662003709 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 420662003710 TPR motif; other site 420662003711 binding surface 420662003712 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 420662003713 Tetratricopeptide repeat; Region: TPR_12; pfam13424 420662003714 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 420662003715 binding surface 420662003716 TPR motif; other site 420662003717 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 420662003718 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662003719 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662003720 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 420662003721 apolar tunnel; other site 420662003722 heme binding site [chemical binding]; other site 420662003723 dimerization interface [polypeptide binding]; other site 420662003724 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 420662003725 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 420662003726 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 420662003727 active site 420662003728 DNA binding site [nucleotide binding] 420662003729 Putative phosphatase (DUF442); Region: DUF442; cl17385 420662003730 Yqey-like protein; Region: YqeY; pfam09424 420662003731 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 420662003732 HI0933-like protein; Region: HI0933_like; pfam03486 420662003733 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 420662003734 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662003735 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662003736 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 420662003737 putative effector binding pocket; other site 420662003738 dimerization interface [polypeptide binding]; other site 420662003739 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 420662003740 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 420662003741 putative NAD(P) binding site [chemical binding]; other site 420662003742 dimer interface [polypeptide binding]; other site 420662003743 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 420662003744 Mechanosensitive ion channel; Region: MS_channel; pfam00924 420662003745 Transglycosylase SLT domain; Region: SLT_2; pfam13406 420662003746 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 420662003747 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662003748 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 420662003749 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662003750 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662003751 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 420662003752 Protein of unknown function DUF58; Region: DUF58; pfam01882 420662003753 MoxR-like ATPases [General function prediction only]; Region: COG0714 420662003754 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 420662003755 Walker A motif; other site 420662003756 ATP binding site [chemical binding]; other site 420662003757 Walker B motif; other site 420662003758 arginine finger; other site 420662003759 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 420662003760 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 420662003761 putative active site [active] 420662003762 Zn binding site [ion binding]; other site 420662003763 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 420662003764 Mechanosensitive ion channel; Region: MS_channel; pfam00924 420662003765 BAX inhibitor (BI)-1/YccA-like protein family; Region: BI-1-like; cl00473 420662003766 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 420662003767 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 420662003768 ATP binding site [chemical binding]; other site 420662003769 Mg2+ binding site [ion binding]; other site 420662003770 G-X-G motif; other site 420662003771 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662003772 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 420662003773 active site 420662003774 phosphorylation site [posttranslational modification] 420662003775 intermolecular recognition site; other site 420662003776 dimerization interface [polypeptide binding]; other site 420662003777 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 420662003778 DNA binding residues [nucleotide binding] 420662003779 dimerization interface [polypeptide binding]; other site 420662003780 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 420662003781 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 420662003782 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 420662003783 NAD(P) binding site [chemical binding]; other site 420662003784 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 420662003785 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 420662003786 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 420662003787 S-adenosylmethionine binding site [chemical binding]; other site 420662003788 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 420662003789 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 420662003790 Peptidase family M23; Region: Peptidase_M23; pfam01551 420662003791 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 420662003792 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 420662003793 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662003794 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 420662003795 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 420662003796 DNA binding residues [nucleotide binding] 420662003797 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 420662003798 TRAM domain; Region: TRAM; cl01282 420662003799 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 420662003800 S-adenosylmethionine binding site [chemical binding]; other site 420662003801 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 420662003802 YccA-like proteins; Region: YccA_like; cd10433 420662003803 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 420662003804 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 420662003805 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 420662003806 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 420662003807 heme binding site [chemical binding]; other site 420662003808 ferroxidase pore; other site 420662003809 ferroxidase diiron center [ion binding]; other site 420662003810 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 420662003811 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 420662003812 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 420662003813 catalytic site [active] 420662003814 subunit interface [polypeptide binding]; other site 420662003815 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 420662003816 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 420662003817 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 420662003818 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 420662003819 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 420662003820 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662003821 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 420662003822 IMP binding site; other site 420662003823 dimer interface [polypeptide binding]; other site 420662003824 interdomain contacts; other site 420662003825 partial ornithine binding site; other site 420662003826 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 420662003827 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 420662003828 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 420662003829 Protein of unknown function (DUF502); Region: DUF502; cl01107 420662003830 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 420662003831 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 420662003832 FtsJ-like methyltransferase; Region: FtsJ; cl17430 420662003833 FtsH Extracellular; Region: FtsH_ext; pfam06480 420662003834 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 420662003835 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 420662003836 Walker A motif; other site 420662003837 ATP binding site [chemical binding]; other site 420662003838 Walker B motif; other site 420662003839 arginine finger; other site 420662003840 Peptidase family M41; Region: Peptidase_M41; pfam01434 420662003841 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 420662003842 dihydropteroate synthase; Region: DHPS; TIGR01496 420662003843 substrate binding pocket [chemical binding]; other site 420662003844 dimer interface [polypeptide binding]; other site 420662003845 inhibitor binding site; inhibition site 420662003846 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 420662003847 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 420662003848 active site 420662003849 substrate binding site [chemical binding]; other site 420662003850 metal binding site [ion binding]; metal-binding site 420662003851 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 420662003852 Fasciclin domain; Region: Fasciclin; pfam02469 420662003853 PBP superfamily domain; Region: PBP_like_2; cl17296 420662003854 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 420662003855 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 420662003856 dimer interface [polypeptide binding]; other site 420662003857 conserved gate region; other site 420662003858 putative PBP binding loops; other site 420662003859 ABC-ATPase subunit interface; other site 420662003860 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 420662003861 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 420662003862 dimer interface [polypeptide binding]; other site 420662003863 conserved gate region; other site 420662003864 putative PBP binding loops; other site 420662003865 ABC-ATPase subunit interface; other site 420662003866 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 420662003867 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 420662003868 Walker A/P-loop; other site 420662003869 ATP binding site [chemical binding]; other site 420662003870 Q-loop/lid; other site 420662003871 ABC transporter signature motif; other site 420662003872 Walker B; other site 420662003873 D-loop; other site 420662003874 H-loop/switch region; other site 420662003875 transcriptional regulator PhoU; Provisional; Region: PRK11115 420662003876 PhoU domain; Region: PhoU; pfam01895 420662003877 PhoU domain; Region: PhoU; pfam01895 420662003878 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 420662003879 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 420662003880 active site 420662003881 phosphorylation site [posttranslational modification] 420662003882 intermolecular recognition site; other site 420662003883 dimerization interface [polypeptide binding]; other site 420662003884 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 420662003885 DNA binding site [nucleotide binding] 420662003886 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 420662003887 PAS domain; Region: PAS; smart00091 420662003888 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 420662003889 dimer interface [polypeptide binding]; other site 420662003890 phosphorylation site [posttranslational modification] 420662003891 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 420662003892 ATP binding site [chemical binding]; other site 420662003893 G-X-G motif; other site 420662003894 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 420662003895 putative efflux protein, MATE family; Region: matE; TIGR00797 420662003896 cation binding site [ion binding]; other site 420662003897 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 420662003898 transcription termination factor Rho; Provisional; Region: rho; PRK09376 420662003899 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 420662003900 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 420662003901 RNA binding site [nucleotide binding]; other site 420662003902 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 420662003903 multimer interface [polypeptide binding]; other site 420662003904 Walker A motif; other site 420662003905 ATP binding site [chemical binding]; other site 420662003906 Walker B motif; other site 420662003907 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 420662003908 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662003909 catalytic residues [active] 420662003910 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 420662003911 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 420662003912 Part of AAA domain; Region: AAA_19; pfam13245 420662003913 Family description; Region: UvrD_C_2; pfam13538 420662003914 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 420662003915 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 420662003916 catalytic residues [active] 420662003917 substrate binding pocket [chemical binding]; other site 420662003918 substrate-Mg2+ binding site; other site 420662003919 aspartate-rich region 1; other site 420662003920 aspartate-rich region 2; other site 420662003921 squalene synthase HpnC; Region: HpnC; TIGR03464 420662003922 substrate binding pocket [chemical binding]; other site 420662003923 substrate-Mg2+ binding site; other site 420662003924 aspartate-rich region 1; other site 420662003925 aspartate-rich region 2; other site 420662003926 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662003927 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662003928 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662003929 putative membrane fusion protein; Region: TIGR02828 420662003930 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 420662003931 trigger factor; Provisional; Region: tig; PRK01490 420662003932 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 420662003933 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 420662003934 Clp protease; Region: CLP_protease; pfam00574 420662003935 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 420662003936 oligomer interface [polypeptide binding]; other site 420662003937 active site residues [active] 420662003938 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 420662003939 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 420662003940 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 420662003941 Walker A motif; other site 420662003942 ATP binding site [chemical binding]; other site 420662003943 Walker B motif; other site 420662003944 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 420662003945 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 420662003946 Found in ATP-dependent protease La (LON); Region: LON; smart00464 420662003947 Found in ATP-dependent protease La (LON); Region: LON; smart00464 420662003948 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 420662003949 Walker A motif; other site 420662003950 ATP binding site [chemical binding]; other site 420662003951 Walker B motif; other site 420662003952 arginine finger; other site 420662003953 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 420662003954 glutamate racemase; Provisional; Region: PRK00865 420662003955 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 420662003956 Ligand binding site [chemical binding]; other site 420662003957 Electron transfer flavoprotein domain; Region: ETF; pfam01012 420662003958 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 420662003959 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 420662003960 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 420662003961 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 420662003962 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 420662003963 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 420662003964 active site 420662003965 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 420662003966 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 420662003967 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 420662003968 FMN binding site [chemical binding]; other site 420662003969 substrate binding site [chemical binding]; other site 420662003970 putative catalytic residue [active] 420662003971 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 420662003972 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 420662003973 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 420662003974 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 420662003975 Dodecin; Region: Dodecin; pfam07311 420662003976 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 420662003977 Peptidase family M48; Region: Peptidase_M48; pfam01435 420662003978 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 420662003979 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 420662003980 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 420662003981 active site 420662003982 catalytic tetrad [active] 420662003983 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662003984 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 420662003985 C-terminal domain interface [polypeptide binding]; other site 420662003986 GSH binding site (G-site) [chemical binding]; other site 420662003987 dimer interface [polypeptide binding]; other site 420662003988 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 420662003989 N-terminal domain interface [polypeptide binding]; other site 420662003990 dimer interface [polypeptide binding]; other site 420662003991 substrate binding pocket (H-site) [chemical binding]; other site 420662003992 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 420662003993 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 420662003994 active site 420662003995 HIGH motif; other site 420662003996 nucleotide binding site [chemical binding]; other site 420662003997 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 420662003998 KMSKS motif; other site 420662003999 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 420662004000 Phosphopantetheine attachment site; Region: PP-binding; cl09936 420662004001 Predicted membrane protein [Function unknown]; Region: COG4648 420662004002 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662004003 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 420662004004 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662004005 acyl-activating enzyme (AAE) consensus motif; other site 420662004006 AMP binding site [chemical binding]; other site 420662004007 active site 420662004008 acyl-activating enzyme (AAE) consensus motif; other site 420662004009 CoA binding site [chemical binding]; other site 420662004010 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 420662004011 active site 2 [active] 420662004012 active site 1 [active] 420662004013 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 420662004014 putative acyl-acceptor binding pocket; other site 420662004015 Predicted exporter [General function prediction only]; Region: COG4258 420662004016 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 420662004017 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 420662004018 NodB motif; other site 420662004019 active site 420662004020 catalytic site [active] 420662004021 metal binding site [ion binding]; metal-binding site 420662004022 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 420662004023 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 420662004024 dimer interface [polypeptide binding]; other site 420662004025 active site 420662004026 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 420662004027 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 420662004028 putative active site 1 [active] 420662004029 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 420662004030 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662004031 NAD(P) binding site [chemical binding]; other site 420662004032 active site 420662004033 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662004034 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 420662004035 Ligand binding site; other site 420662004036 Putative Catalytic site; other site 420662004037 DXD motif; other site 420662004038 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 420662004039 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 420662004040 putative acyl-acceptor binding pocket; other site 420662004041 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 420662004042 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_5; cd06153 420662004043 homotrimer interaction site [polypeptide binding]; other site 420662004044 putative active site [active] 420662004045 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 420662004046 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 420662004047 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 420662004048 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 420662004049 S-adenosylmethionine binding site [chemical binding]; other site 420662004050 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662004051 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662004052 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662004053 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 420662004054 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 420662004055 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 420662004056 hypothetical protein; Validated; Region: PRK00110 420662004057 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 420662004058 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 420662004059 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 420662004060 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 420662004061 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 420662004062 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 420662004063 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 420662004064 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 420662004065 active site 420662004066 (T/H)XGH motif; other site 420662004067 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 420662004068 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 420662004069 Maf-like protein; Region: Maf; pfam02545 420662004070 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 420662004071 active site 420662004072 dimer interface [polypeptide binding]; other site 420662004073 ribonuclease G; Provisional; Region: PRK11712 420662004074 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 420662004075 homodimer interface [polypeptide binding]; other site 420662004076 oligonucleotide binding site [chemical binding]; other site 420662004077 translocation protein TolB; Provisional; Region: tolB; PRK02889 420662004078 TolB amino-terminal domain; Region: TolB_N; pfam04052 420662004079 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 420662004080 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 420662004081 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 420662004082 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 420662004083 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 420662004084 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662004085 ligand binding site [chemical binding]; other site 420662004086 Protein of unknown function (DUF972); Region: DUF972; pfam06156 420662004087 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 420662004088 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 420662004089 binding surface 420662004090 TPR motif; other site 420662004091 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 420662004092 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 420662004093 ATP binding site [chemical binding]; other site 420662004094 substrate interface [chemical binding]; other site 420662004095 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 420662004096 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662004097 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662004098 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 420662004099 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 420662004100 Hemerythrin-like domain; Region: Hr-like; cd12108 420662004101 Fe binding site [ion binding]; other site 420662004102 Protein of unknown function (DUF454); Region: DUF454; cl01063 420662004103 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 420662004104 ArsC family; Region: ArsC; pfam03960 420662004105 putative catalytic residues [active] 420662004106 aconitate hydratase; Validated; Region: PRK09277 420662004107 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 420662004108 substrate binding site [chemical binding]; other site 420662004109 ligand binding site [chemical binding]; other site 420662004110 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 420662004111 substrate binding site [chemical binding]; other site 420662004112 DNA ligase; Provisional; Region: PRK09125 420662004113 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 420662004114 DNA binding site [nucleotide binding] 420662004115 active site 420662004116 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 420662004117 DNA binding site [nucleotide binding] 420662004118 exonuclease I; Provisional; Region: sbcB; PRK11779 420662004119 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 420662004120 active site 420662004121 catalytic site [active] 420662004122 substrate binding site [chemical binding]; other site 420662004123 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 420662004124 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 420662004125 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 420662004126 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 420662004127 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 420662004128 Predicted membrane protein [Function unknown]; Region: COG1289 420662004129 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 420662004130 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 420662004131 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 420662004132 substrate binding site [chemical binding]; other site 420662004133 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 420662004134 substrate binding site [chemical binding]; other site 420662004135 ligand binding site [chemical binding]; other site 420662004136 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB-like; cd09875 420662004137 putative active site [active] 420662004138 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 420662004139 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 420662004140 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 420662004141 catalytic loop [active] 420662004142 iron binding site [ion binding]; other site 420662004143 Protein of unknown function (DUF808); Region: DUF808; pfam05661 420662004144 H-NS histone family; Region: Histone_HNS; pfam00816 420662004145 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 420662004146 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 420662004147 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 420662004148 oxidative damage protection protein; Provisional; Region: PRK05408 420662004149 N-acetylglutamate synthase; Validated; Region: PRK05279 420662004150 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 420662004151 putative feedback inhibition sensing region; other site 420662004152 putative nucleotide binding site [chemical binding]; other site 420662004153 putative substrate binding site [chemical binding]; other site 420662004154 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662004155 Coenzyme A binding pocket [chemical binding]; other site 420662004156 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 420662004157 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 420662004158 ATP binding site [chemical binding]; other site 420662004159 putative Mg++ binding site [ion binding]; other site 420662004160 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 420662004161 nucleotide binding region [chemical binding]; other site 420662004162 ATP-binding site [chemical binding]; other site 420662004163 Helicase associated domain (HA2); Region: HA2; pfam04408 420662004164 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 420662004165 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 420662004166 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 420662004167 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662004168 Cache domain; Region: Cache_1; pfam02743 420662004169 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 420662004170 dimer interface [polypeptide binding]; other site 420662004171 phosphorylation site [posttranslational modification] 420662004172 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 420662004173 ATP binding site [chemical binding]; other site 420662004174 Mg2+ binding site [ion binding]; other site 420662004175 G-X-G motif; other site 420662004176 Response regulator receiver domain; Region: Response_reg; pfam00072 420662004177 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 420662004178 active site 420662004179 phosphorylation site [posttranslational modification] 420662004180 intermolecular recognition site; other site 420662004181 dimerization interface [polypeptide binding]; other site 420662004182 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 420662004183 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 420662004184 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 420662004185 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 420662004186 Domain of unknown function (DUF427); Region: DUF427; pfam04248 420662004187 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 420662004188 fumarate hydratase FumA; Provisional; Region: PRK15390 420662004189 Fumarase C-terminus; Region: Fumerase_C; pfam05683 420662004190 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 420662004191 hypothetical protein; Provisional; Region: PRK05208 420662004192 acetyl-CoA synthetase; Provisional; Region: PRK00174 420662004193 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 420662004194 active site 420662004195 CoA binding site [chemical binding]; other site 420662004196 acyl-activating enzyme (AAE) consensus motif; other site 420662004197 AMP binding site [chemical binding]; other site 420662004198 acetate binding site [chemical binding]; other site 420662004199 Cytochrome c; Region: Cytochrom_C; cl11414 420662004200 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 420662004201 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 420662004202 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662004203 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 420662004204 dimerization interface [polypeptide binding]; other site 420662004205 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 420662004206 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 420662004207 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662004208 Walker A/P-loop; other site 420662004209 ATP binding site [chemical binding]; other site 420662004210 Q-loop/lid; other site 420662004211 ABC transporter signature motif; other site 420662004212 Walker B; other site 420662004213 D-loop; other site 420662004214 H-loop/switch region; other site 420662004215 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662004216 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 420662004217 dimer interface [polypeptide binding]; other site 420662004218 conserved gate region; other site 420662004219 putative PBP binding loops; other site 420662004220 ABC-ATPase subunit interface; other site 420662004221 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 420662004222 NMT1-like family; Region: NMT1_2; pfam13379 420662004223 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 420662004224 ANTAR domain; Region: ANTAR; pfam03861 420662004225 oxidoreductase, 2OG-Fe(II) oxygenase family protein; Region: PLN00417 420662004226 UGMP family protein; Validated; Region: PRK09604 420662004227 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 420662004228 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 420662004229 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 420662004230 putative dimer interface [polypeptide binding]; other site 420662004231 aspartate aminotransferase; Provisional; Region: PRK06108 420662004232 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 420662004233 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004234 homodimer interface [polypeptide binding]; other site 420662004235 catalytic residue [active] 420662004236 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 420662004237 16S/18S rRNA binding site [nucleotide binding]; other site 420662004238 S13e-L30e interaction site [polypeptide binding]; other site 420662004239 25S rRNA binding site [nucleotide binding]; other site 420662004240 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 420662004241 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 420662004242 RNase E interface [polypeptide binding]; other site 420662004243 trimer interface [polypeptide binding]; other site 420662004244 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 420662004245 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 420662004246 RNase E interface [polypeptide binding]; other site 420662004247 trimer interface [polypeptide binding]; other site 420662004248 active site 420662004249 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 420662004250 putative nucleic acid binding region [nucleotide binding]; other site 420662004251 G-X-X-G motif; other site 420662004252 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 420662004253 RNA binding site [nucleotide binding]; other site 420662004254 domain interface; other site 420662004255 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 420662004256 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 420662004257 NAD(P) binding site [chemical binding]; other site 420662004258 triosephosphate isomerase; Provisional; Region: PRK14567 420662004259 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 420662004260 substrate binding site [chemical binding]; other site 420662004261 dimer interface [polypeptide binding]; other site 420662004262 catalytic triad [active] 420662004263 Preprotein translocase SecG subunit; Region: SecG; pfam03840 420662004264 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 420662004265 NADH dehydrogenase subunit B; Validated; Region: PRK06411 420662004266 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 420662004267 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 420662004268 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 420662004269 NADH dehydrogenase subunit D; Validated; Region: PRK06075 420662004270 NADH dehydrogenase subunit E; Validated; Region: PRK07539 420662004271 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 420662004272 putative dimer interface [polypeptide binding]; other site 420662004273 [2Fe-2S] cluster binding site [ion binding]; other site 420662004274 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 420662004275 SLBB domain; Region: SLBB; pfam10531 420662004276 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 420662004277 NADH dehydrogenase subunit G; Validated; Region: PRK09129 420662004278 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 420662004279 catalytic loop [active] 420662004280 iron binding site [ion binding]; other site 420662004281 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 420662004282 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 420662004283 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 420662004284 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 420662004285 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 420662004286 4Fe-4S binding domain; Region: Fer4; cl02805 420662004287 4Fe-4S binding domain; Region: Fer4; pfam00037 420662004288 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 420662004289 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 420662004290 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 420662004291 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 420662004292 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 420662004293 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 420662004294 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 420662004295 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 420662004296 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 420662004297 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 420662004298 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 420662004299 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 420662004300 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 420662004301 dimer interface [polypeptide binding]; other site 420662004302 ADP-ribose binding site [chemical binding]; other site 420662004303 active site 420662004304 nudix motif; other site 420662004305 metal binding site [ion binding]; metal-binding site 420662004306 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 420662004307 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 420662004308 FAD binding domain; Region: FAD_binding_4; pfam01565 420662004309 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 420662004310 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 420662004311 FOG: CBS domain [General function prediction only]; Region: COG0517 420662004312 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; cl15354 420662004313 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 420662004314 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 420662004315 Tetramer interface [polypeptide binding]; other site 420662004316 active site 420662004317 FMN-binding site [chemical binding]; other site 420662004318 Cupin domain; Region: Cupin_2; cl17218 420662004319 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 420662004320 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 420662004321 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 420662004322 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 420662004323 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 420662004324 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 420662004325 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 420662004326 tetramer interface [polypeptide binding]; other site 420662004327 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004328 catalytic residue [active] 420662004329 glycine dehydrogenase; Provisional; Region: PRK05367 420662004330 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 420662004331 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662004332 catalytic residue [active] 420662004333 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 420662004334 tetramer interface [polypeptide binding]; other site 420662004335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004336 catalytic residue [active] 420662004337 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 420662004338 lipoyl attachment site [posttranslational modification]; other site 420662004339 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 420662004340 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 420662004341 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 420662004342 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 420662004343 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 420662004344 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662004345 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662004346 metal binding site [ion binding]; metal-binding site 420662004347 active site 420662004348 I-site; other site 420662004349 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 420662004350 acyl-CoA synthetase; Validated; Region: PRK08162 420662004351 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 420662004352 acyl-activating enzyme (AAE) consensus motif; other site 420662004353 putative active site [active] 420662004354 AMP binding site [chemical binding]; other site 420662004355 putative CoA binding site [chemical binding]; other site 420662004356 enoyl-CoA hydratase; Validated; Region: PRK08139 420662004357 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 420662004358 substrate binding site [chemical binding]; other site 420662004359 oxyanion hole (OAH) forming residues; other site 420662004360 trimer interface [polypeptide binding]; other site 420662004361 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 420662004362 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662004363 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 420662004364 G1 box; other site 420662004365 GTP/Mg2+ binding site [chemical binding]; other site 420662004366 G2 box; other site 420662004367 Switch I region; other site 420662004368 G3 box; other site 420662004369 Switch II region; other site 420662004370 G4 box; other site 420662004371 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 420662004372 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 420662004373 Beta-lactamase; Region: Beta-lactamase; pfam00144 420662004374 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 420662004375 Prostaglandin dehydrogenases; Region: PGDH; cd05288 420662004376 NAD(P) binding site [chemical binding]; other site 420662004377 substrate binding site [chemical binding]; other site 420662004378 dimer interface [polypeptide binding]; other site 420662004379 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 420662004380 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 420662004381 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 420662004382 Domain of unknown function (DUF4331); Region: DUF4331; pfam14224 420662004383 short chain dehydrogenase; Provisional; Region: PRK06949 420662004384 classical (c) SDRs; Region: SDR_c; cd05233 420662004385 NAD(P) binding site [chemical binding]; other site 420662004386 active site 420662004387 hypothetical protein; Provisional; Region: PRK11239 420662004388 Protein of unknown function, DUF480; Region: DUF480; pfam04337 420662004389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5267 420662004390 Protein of unknown function (DUF1501); Region: DUF1501; pfam07394 420662004391 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662004392 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 420662004393 lysophospholipid transporter LplT; Provisional; Region: PRK11195 420662004394 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 420662004395 PAS domain; Region: PAS_9; pfam13426 420662004396 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 420662004397 putative active site [active] 420662004398 heme pocket [chemical binding]; other site 420662004399 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 420662004400 DNA binding residues [nucleotide binding] 420662004401 dimerization interface [polypeptide binding]; other site 420662004402 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 420662004403 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 420662004404 Imelysin; Region: Peptidase_M75; cl09159 420662004405 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 420662004406 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 420662004407 Imelysin; Region: Peptidase_M75; pfam09375 420662004408 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 420662004409 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 420662004410 dimer interface [polypeptide binding]; other site 420662004411 Uncharacterized conserved protein [Function unknown]; Region: COG2353 420662004412 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 420662004413 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 420662004414 non-specific DNA binding site [nucleotide binding]; other site 420662004415 salt bridge; other site 420662004416 sequence-specific DNA binding site [nucleotide binding]; other site 420662004417 Integrase core domain; Region: rve; pfam00665 420662004418 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 420662004419 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 420662004420 Walker A motif; other site 420662004421 ATP binding site [chemical binding]; other site 420662004422 Walker B motif; other site 420662004423 arginine finger; other site 420662004424 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 420662004425 inhibitor-cofactor binding pocket; inhibition site 420662004426 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004427 catalytic residue [active] 420662004428 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662004429 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662004430 The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; Region: PBP2_LrhA_like; cd08439 420662004431 putative dimerization interface [polypeptide binding]; other site 420662004432 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 420662004433 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 420662004434 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 420662004435 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 420662004436 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 420662004437 ferrous iron transporter FeoB; Region: feoB; TIGR00437 420662004438 G1 box; other site 420662004439 GTP/Mg2+ binding site [chemical binding]; other site 420662004440 Switch I region; other site 420662004441 G2 box; other site 420662004442 G3 box; other site 420662004443 Switch II region; other site 420662004444 G4 box; other site 420662004445 G5 box; other site 420662004446 Nucleoside recognition; Region: Gate; pfam07670 420662004447 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 420662004448 Nucleoside recognition; Region: Gate; pfam07670 420662004449 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 420662004450 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 420662004451 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 420662004452 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 420662004453 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 420662004454 Cytochrome c; Region: Cytochrom_C; cl11414 420662004455 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662004456 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662004457 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 420662004458 putative dimerization interface [polypeptide binding]; other site 420662004459 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 420662004460 Ribulose bisphosphate carboxylase large chain, Form I; Region: RuBisCO_large_I; cd08212 420662004461 homodimer interface [polypeptide binding]; other site 420662004462 active site 420662004463 heterodimer interface [polypeptide binding]; other site 420662004464 catalytic residue [active] 420662004465 metal binding site [ion binding]; metal-binding site 420662004466 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 420662004467 multimerization interface [polypeptide binding]; other site 420662004468 CbbX; Provisional; Region: cbbX; CHL00181 420662004469 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 420662004470 Walker A motif; other site 420662004471 ATP binding site [chemical binding]; other site 420662004472 Walker B motif; other site 420662004473 arginine finger; other site 420662004474 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 420662004475 AMP binding site [chemical binding]; other site 420662004476 metal binding site [ion binding]; metal-binding site 420662004477 active site 420662004478 Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to...; Region: PRK_like; cd02029 420662004479 phosphoglycolate phosphatase; Provisional; Region: PRK13222 420662004480 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 420662004481 motif II; other site 420662004482 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 420662004483 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 420662004484 motif II; other site 420662004485 Caspase domain; Region: Peptidase_C14; pfam00656 420662004486 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 420662004487 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 420662004488 putative catalytic residue [active] 420662004489 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 420662004490 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 420662004491 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 420662004492 DsbD alpha interface [polypeptide binding]; other site 420662004493 catalytic residues [active] 420662004494 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 420662004495 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662004496 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662004497 active site 420662004498 ATP binding site [chemical binding]; other site 420662004499 substrate binding site [chemical binding]; other site 420662004500 activation loop (A-loop); other site 420662004501 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 420662004502 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 420662004503 N-terminal plug; other site 420662004504 ligand-binding site [chemical binding]; other site 420662004505 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 420662004506 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662004507 Ferredoxin [Energy production and conversion]; Region: COG1146 420662004508 4Fe-4S binding domain; Region: Fer4; cl02805 420662004509 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 420662004510 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 420662004511 active site 420662004512 SAM binding site [chemical binding]; other site 420662004513 homodimer interface [polypeptide binding]; other site 420662004514 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 420662004515 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 420662004516 CysD dimerization site [polypeptide binding]; other site 420662004517 G1 box; other site 420662004518 putative GEF interaction site [polypeptide binding]; other site 420662004519 GTP/Mg2+ binding site [chemical binding]; other site 420662004520 Switch I region; other site 420662004521 G2 box; other site 420662004522 G3 box; other site 420662004523 Switch II region; other site 420662004524 G4 box; other site 420662004525 G5 box; other site 420662004526 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 420662004527 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 420662004528 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 420662004529 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 420662004530 Active Sites [active] 420662004531 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 420662004532 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 420662004533 Active Sites [active] 420662004534 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 420662004535 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 420662004536 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 420662004537 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 420662004538 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 420662004539 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 420662004540 nucleophile elbow; other site 420662004541 Phasin protein; Region: Phasin_2; pfam09361 420662004542 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 420662004543 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 420662004544 putative active site [active] 420662004545 Zn binding site [ion binding]; other site 420662004546 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 420662004547 active site 420662004548 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 420662004549 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 420662004550 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 420662004551 transmembrane helices; other site 420662004552 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 420662004553 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 420662004554 dimerization interface [polypeptide binding]; other site 420662004555 ligand binding site [chemical binding]; other site 420662004556 NADP binding site [chemical binding]; other site 420662004557 catalytic site [active] 420662004558 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 420662004559 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 420662004560 N-terminal plug; other site 420662004561 ligand-binding site [chemical binding]; other site 420662004562 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 420662004563 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 420662004564 RmuC family; Region: RmuC; pfam02646 420662004565 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 420662004566 putative active site [active] 420662004567 putative metal binding site [ion binding]; other site 420662004568 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 420662004569 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 420662004570 ATP binding site [chemical binding]; other site 420662004571 putative Mg++ binding site [ion binding]; other site 420662004572 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 420662004573 nucleotide binding region [chemical binding]; other site 420662004574 ATP-binding site [chemical binding]; other site 420662004575 DEAD/H associated; Region: DEAD_assoc; pfam08494 420662004576 ATP-dependent DNA ligase; Validated; Region: PRK09247 420662004577 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 420662004578 active site 420662004579 DNA binding site [nucleotide binding] 420662004580 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 420662004581 DNA binding site [nucleotide binding] 420662004582 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 420662004583 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 420662004584 PEP synthetase regulatory protein; Provisional; Region: PRK05339 420662004585 phosphoenolpyruvate synthase; Validated; Region: PRK06464 420662004586 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 420662004587 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 420662004588 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 420662004589 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 420662004590 TPR motif; other site 420662004591 binding surface 420662004592 TPR repeat; Region: TPR_11; pfam13414 420662004593 TPR repeat; Region: TPR_11; pfam13414 420662004594 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 420662004595 binding surface 420662004596 TPR motif; other site 420662004597 Tetratricopeptide repeat; Region: TPR_16; pfam13432 420662004598 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 420662004599 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 420662004600 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 420662004601 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 420662004602 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 420662004603 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 420662004604 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 420662004605 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 420662004606 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 420662004607 replicative DNA helicase; Region: DnaB; TIGR00665 420662004608 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 420662004609 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 420662004610 Walker A motif; other site 420662004611 ATP binding site [chemical binding]; other site 420662004612 Walker B motif; other site 420662004613 DNA binding loops [nucleotide binding] 420662004614 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 420662004615 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 420662004616 putative active site [active] 420662004617 putative PHP Thumb interface [polypeptide binding]; other site 420662004618 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 420662004619 generic binding surface I; other site 420662004620 generic binding surface II; other site 420662004621 DNA Polymerase Y-family; Region: PolY_like; cd03468 420662004622 active site 420662004623 DNA binding site [nucleotide binding] 420662004624 Uncharacterized conserved protein [Function unknown]; Region: COG4544 420662004625 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 420662004626 beta-ketothiolase; Provisional; Region: PRK09051 420662004627 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 420662004628 dimer interface [polypeptide binding]; other site 420662004629 active site 420662004630 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 420662004631 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 420662004632 putative active site [active] 420662004633 PhoH-like protein; Region: PhoH; pfam02562 420662004634 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 420662004635 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 420662004636 catalytic triad [active] 420662004637 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 420662004638 aminotransferase AlaT; Validated; Region: PRK09265 420662004639 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 420662004640 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004641 homodimer interface [polypeptide binding]; other site 420662004642 catalytic residue [active] 420662004643 homoserine dehydrogenase; Provisional; Region: PRK06349 420662004644 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 420662004645 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 420662004646 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 420662004647 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 420662004648 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 420662004649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662004650 catalytic residue [active] 420662004651 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 420662004652 Walker A motif; other site 420662004653 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 420662004654 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 420662004655 dimer interface [polypeptide binding]; other site 420662004656 putative functional site; other site 420662004657 putative MPT binding site; other site 420662004658 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 420662004659 MoaE interaction surface [polypeptide binding]; other site 420662004660 MoeB interaction surface [polypeptide binding]; other site 420662004661 thiocarboxylated glycine; other site 420662004662 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662004663 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 420662004664 active site 420662004665 ATP binding site [chemical binding]; other site 420662004666 substrate binding site [chemical binding]; other site 420662004667 activation loop (A-loop); other site 420662004668 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 420662004669 MoaE homodimer interface [polypeptide binding]; other site 420662004670 MoaD interaction [polypeptide binding]; other site 420662004671 active site residues [active] 420662004672 chromosome condensation membrane protein; Provisional; Region: PRK14196 420662004673 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 420662004674 Clp amino terminal domain; Region: Clp_N; pfam02861 420662004675 Clp amino terminal domain; Region: Clp_N; pfam02861 420662004676 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 420662004677 Walker A motif; other site 420662004678 ATP binding site [chemical binding]; other site 420662004679 Walker B motif; other site 420662004680 arginine finger; other site 420662004681 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 420662004682 Walker A motif; other site 420662004683 ATP binding site [chemical binding]; other site 420662004684 Walker B motif; other site 420662004685 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 420662004686 L-aspartate oxidase; Provisional; Region: PRK06175 420662004687 L-aspartate oxidase; Provisional; Region: PRK09077 420662004688 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 420662004689 Late competence development protein ComFB; Region: ComFB; pfam10719 420662004690 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 420662004691 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 420662004692 dimerization interface [polypeptide binding]; other site 420662004693 active site 420662004694 quinolinate synthetase; Provisional; Region: PRK09375 420662004695 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 420662004696 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 420662004697 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 420662004698 Major Facilitator Superfamily; Region: MFS_1; pfam07690 420662004699 putative substrate translocation pore; other site 420662004700 thiamine pyrophosphate protein; Validated; Region: PRK08199 420662004701 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 420662004702 PYR/PP interface [polypeptide binding]; other site 420662004703 dimer interface [polypeptide binding]; other site 420662004704 TPP binding site [chemical binding]; other site 420662004705 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 420662004706 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 420662004707 TPP-binding site [chemical binding]; other site 420662004708 META domain; Region: META; pfam03724 420662004709 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 420662004710 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 420662004711 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 420662004712 putative DNA binding site [nucleotide binding]; other site 420662004713 putative Zn2+ binding site [ion binding]; other site 420662004714 AsnC family; Region: AsnC_trans_reg; pfam01037 420662004715 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 420662004716 Predicted integral membrane protein [Function unknown]; Region: COG0392 420662004717 Uncharacterized conserved protein [Function unknown]; Region: COG2898 420662004718 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 420662004719 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 420662004720 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 420662004721 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 420662004722 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 420662004723 catalytic residues [active] 420662004724 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 420662004725 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 420662004726 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 420662004727 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662004728 putative C-terminal domain interface [polypeptide binding]; other site 420662004729 putative GSH binding site (G-site) [chemical binding]; other site 420662004730 putative dimer interface [polypeptide binding]; other site 420662004731 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 420662004732 putative N-terminal domain interface [polypeptide binding]; other site 420662004733 putative dimer interface [polypeptide binding]; other site 420662004734 putative substrate binding pocket (H-site) [chemical binding]; other site 420662004735 Cupin domain; Region: Cupin_2; cl17218 420662004736 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 420662004737 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 420662004738 motif II; other site 420662004739 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 420662004740 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 420662004741 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 420662004742 ATP binding site [chemical binding]; other site 420662004743 putative Mg++ binding site [ion binding]; other site 420662004744 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 420662004745 nucleotide binding region [chemical binding]; other site 420662004746 ATP-binding site [chemical binding]; other site 420662004747 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 420662004748 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 420662004749 substrate binding site; other site 420662004750 dimer interface; other site 420662004751 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 420662004752 homotrimer interaction site [polypeptide binding]; other site 420662004753 zinc binding site [ion binding]; other site 420662004754 CDP-binding sites; other site 420662004755 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 420662004756 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 420662004757 dimerization interface [polypeptide binding]; other site 420662004758 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 420662004759 dimer interface [polypeptide binding]; other site 420662004760 phosphorylation site [posttranslational modification] 420662004761 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 420662004762 ATP binding site [chemical binding]; other site 420662004763 Mg2+ binding site [ion binding]; other site 420662004764 G-X-G motif; other site 420662004765 osmolarity response regulator; Provisional; Region: ompR; PRK09468 420662004766 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 420662004767 active site 420662004768 phosphorylation site [posttranslational modification] 420662004769 intermolecular recognition site; other site 420662004770 dimerization interface [polypeptide binding]; other site 420662004771 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 420662004772 DNA binding site [nucleotide binding] 420662004773 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 420662004774 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 420662004775 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 420662004776 NAD binding site [chemical binding]; other site 420662004777 homotetramer interface [polypeptide binding]; other site 420662004778 homodimer interface [polypeptide binding]; other site 420662004779 substrate binding site [chemical binding]; other site 420662004780 active site 420662004781 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662004782 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 420662004783 HD domain; Region: HD_4; pfam13328 420662004784 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 420662004785 synthetase active site [active] 420662004786 NTP binding site [chemical binding]; other site 420662004787 metal binding site [ion binding]; metal-binding site 420662004788 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 420662004789 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 420662004790 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 420662004791 putative heme binding pocket [chemical binding]; other site 420662004792 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 420662004793 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662004794 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 420662004795 Sodium Bile acid symporter family; Region: SBF; cl17470 420662004796 Low molecular weight phosphatase family; Region: LMWPc; cd00115 420662004797 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 420662004798 active site 420662004799 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 420662004800 dimerization interface [polypeptide binding]; other site 420662004801 putative DNA binding site [nucleotide binding]; other site 420662004802 putative Zn2+ binding site [ion binding]; other site 420662004803 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 420662004804 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 420662004805 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 420662004806 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 420662004807 Domain of unknown function (DUF336); Region: DUF336; pfam03928 420662004808 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662004809 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 420662004810 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 420662004811 substrate binding pocket [chemical binding]; other site 420662004812 membrane-bound complex binding site; other site 420662004813 hinge residues; other site 420662004814 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662004815 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 420662004816 dimer interface [polypeptide binding]; other site 420662004817 Trp docking motif [polypeptide binding]; other site 420662004818 active site 420662004819 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662004820 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662004821 eyelet of channel; other site 420662004822 trimer interface [polypeptide binding]; other site 420662004823 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662004824 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662004825 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 420662004826 Trp docking motif [polypeptide binding]; other site 420662004827 putative active site [active] 420662004828 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662004829 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 420662004830 Trp docking motif [polypeptide binding]; other site 420662004831 active site 420662004832 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662004833 thiamine monophosphate kinase; Provisional; Region: PRK05731 420662004834 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 420662004835 ATP binding site [chemical binding]; other site 420662004836 dimerization interface [polypeptide binding]; other site 420662004837 lipoyl synthase; Provisional; Region: PRK05481 420662004838 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 420662004839 FeS/SAM binding site; other site 420662004840 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 420662004841 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 420662004842 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 420662004843 E3 interaction surface; other site 420662004844 lipoyl attachment site [posttranslational modification]; other site 420662004845 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 420662004846 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 420662004847 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 420662004848 alpha subunit interface [polypeptide binding]; other site 420662004849 TPP binding site [chemical binding]; other site 420662004850 heterodimer interface [polypeptide binding]; other site 420662004851 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 420662004852 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 420662004853 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 420662004854 tetramer interface [polypeptide binding]; other site 420662004855 TPP-binding site [chemical binding]; other site 420662004856 heterodimer interface [polypeptide binding]; other site 420662004857 phosphorylation loop region [posttranslational modification] 420662004858 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 420662004859 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 420662004860 dimer interface [polypeptide binding]; other site 420662004861 catalytic triad [active] 420662004862 peroxidatic and resolving cysteines [active] 420662004863 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 420662004864 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 420662004865 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 420662004866 dimer interface [polypeptide binding]; other site 420662004867 substrate binding site [chemical binding]; other site 420662004868 ATP binding site [chemical binding]; other site 420662004869 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 420662004870 thiamine phosphate binding site [chemical binding]; other site 420662004871 active site 420662004872 pyrophosphate binding site [ion binding]; other site 420662004873 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 420662004874 ThiS interaction site; other site 420662004875 putative active site [active] 420662004876 tetramer interface [polypeptide binding]; other site 420662004877 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 420662004878 thiS-thiF/thiG interaction site; other site 420662004879 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 420662004880 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 420662004881 ThiC-associated domain; Region: ThiC-associated; pfam13667 420662004882 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 420662004883 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662004884 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 420662004885 Walker A motif; other site 420662004886 ATP binding site [chemical binding]; other site 420662004887 Walker B motif; other site 420662004888 arginine finger; other site 420662004889 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 420662004890 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 420662004891 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 420662004892 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 420662004893 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 420662004894 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 420662004895 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 420662004896 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 420662004897 FeS/SAM binding site; other site 420662004898 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 420662004899 cystathionine beta-lyase; Provisional; Region: PRK07050 420662004900 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662004901 catalytic residue [active] 420662004902 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 420662004903 SmpB-tmRNA interface; other site 420662004904 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 420662004905 putative coenzyme Q binding site [chemical binding]; other site 420662004906 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 420662004907 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 420662004908 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 420662004909 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 420662004910 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 420662004911 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 420662004912 active site 420662004913 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 420662004914 Major Facilitator Superfamily; Region: MFS_1; pfam07690 420662004915 putative substrate translocation pore; other site 420662004916 GMP synthase; Reviewed; Region: guaA; PRK00074 420662004917 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 420662004918 AMP/PPi binding site [chemical binding]; other site 420662004919 candidate oxyanion hole; other site 420662004920 catalytic triad [active] 420662004921 potential glutamine specificity residues [chemical binding]; other site 420662004922 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 420662004923 ATP Binding subdomain [chemical binding]; other site 420662004924 Ligand Binding sites [chemical binding]; other site 420662004925 Dimerization subdomain; other site 420662004926 integrase; Provisional; Region: PRK09692 420662004927 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 420662004928 active site 420662004929 Int/Topo IB signature motif; other site 420662004930 Outer membrane efflux protein; Region: OEP; pfam02321 420662004931 Outer membrane efflux protein; Region: OEP; pfam02321 420662004932 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 420662004933 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662004934 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 420662004935 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 420662004936 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 420662004937 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 420662004938 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 420662004939 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 420662004940 active site 420662004941 phosphorylation site [posttranslational modification] 420662004942 intermolecular recognition site; other site 420662004943 dimerization interface [polypeptide binding]; other site 420662004944 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 420662004945 DNA binding site [nucleotide binding] 420662004946 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 420662004947 HAMP domain; Region: HAMP; pfam00672 420662004948 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 420662004949 dimer interface [polypeptide binding]; other site 420662004950 phosphorylation site [posttranslational modification] 420662004951 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 420662004952 ATP binding site [chemical binding]; other site 420662004953 Mg2+ binding site [ion binding]; other site 420662004954 G-X-G motif; other site 420662004955 Outer membrane efflux protein; Region: OEP; pfam02321 420662004956 Outer membrane efflux protein; Region: OEP; pfam02321 420662004957 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 420662004958 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 420662004959 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 420662004960 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 420662004961 Predicted metal-binding protein [General function prediction only]; Region: COG3019 420662004962 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 420662004963 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 420662004964 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 420662004965 DNA binding residues [nucleotide binding] 420662004966 dimer interface [polypeptide binding]; other site 420662004967 copper binding site [ion binding]; other site 420662004968 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 420662004969 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 420662004970 metal-binding site [ion binding] 420662004971 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 420662004972 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 420662004973 metal-binding site [ion binding] 420662004974 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 420662004975 Soluble P-type ATPase [General function prediction only]; Region: COG4087 420662004976 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 420662004977 metal-binding site [ion binding] 420662004978 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 420662004979 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 420662004980 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 420662004981 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 420662004982 motif II; other site 420662004983 Thioredoxin; Region: Thioredoxin_4; pfam13462 420662004984 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 420662004985 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 420662004986 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 420662004987 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662004988 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662004989 fimbrial outer membrane usher protein; Provisional; Region: PRK15217 420662004990 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662004991 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662004992 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 420662004993 hypothetical protein; Provisional; Region: PRK02237 420662004994 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 420662004995 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 420662004996 DNA binding residues [nucleotide binding] 420662004997 dimer interface [polypeptide binding]; other site 420662004998 putative metal binding site [ion binding]; other site 420662004999 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 420662005000 MPN+ (JAMM) motif; other site 420662005001 Zinc-binding site [ion binding]; other site 420662005002 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 420662005003 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl17483 420662005004 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 420662005005 DNA binding residues [nucleotide binding] 420662005006 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 420662005007 dimer interface [polypeptide binding]; other site 420662005008 mercury binding site [ion binding]; other site 420662005009 MerT mercuric transport protein; Region: MerT; cl03578 420662005010 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 420662005011 metal-binding site [ion binding] 420662005012 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 420662005013 ssDNA binding site [nucleotide binding]; other site 420662005014 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 420662005015 tetramer (dimer of dimers) interface [polypeptide binding]; other site 420662005016 Domain of unknown function (DUF932); Region: DUF932; pfam06067 420662005017 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 420662005018 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 420662005019 ATP binding site [chemical binding]; other site 420662005020 putative Mg++ binding site [ion binding]; other site 420662005021 helicase superfamily c-terminal domain; Region: HELICc; smart00490 420662005022 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 420662005023 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 420662005024 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 420662005025 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662005026 ligand binding site [chemical binding]; other site 420662005027 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 420662005028 Walker A motif; other site 420662005029 ATP binding site [chemical binding]; other site 420662005030 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 420662005031 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 420662005032 Walker A motif; other site 420662005033 hexamer interface [polypeptide binding]; other site 420662005034 ATP binding site [chemical binding]; other site 420662005035 Walker B motif; other site 420662005036 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 420662005037 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 420662005038 VirB7 interaction site; other site 420662005039 VirB8 protein; Region: VirB8; pfam04335 420662005040 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 420662005041 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3602 420662005042 ACT domain; Region: ACT_3; pfam10000 420662005043 Family description; Region: ACT_7; pfam13840 420662005044 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; cl17315 420662005045 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662005046 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 420662005047 active site 420662005048 phosphorylation site [posttranslational modification] 420662005049 intermolecular recognition site; other site 420662005050 dimerization interface [polypeptide binding]; other site 420662005051 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 420662005052 DNA binding residues [nucleotide binding] 420662005053 dimerization interface [polypeptide binding]; other site 420662005054 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 420662005055 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 420662005056 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 420662005057 dimerization interface [polypeptide binding]; other site 420662005058 Histidine kinase; Region: HisKA_3; pfam07730 420662005059 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 420662005060 ATP binding site [chemical binding]; other site 420662005061 Mg2+ binding site [ion binding]; other site 420662005062 G-X-G motif; other site 420662005063 Hemerythrin-like domain; Region: Hr-like; cd12108 420662005064 Fe binding site [ion binding]; other site 420662005065 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 420662005066 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662005067 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 420662005068 ligand binding site [chemical binding]; other site 420662005069 flexible hinge region; other site 420662005070 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 420662005071 putative switch regulator; other site 420662005072 non-specific DNA interactions [nucleotide binding]; other site 420662005073 DNA binding site [nucleotide binding] 420662005074 sequence specific DNA binding site [nucleotide binding]; other site 420662005075 putative cAMP binding site [chemical binding]; other site 420662005076 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 420662005077 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 420662005078 FeS/SAM binding site; other site 420662005079 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 420662005080 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 420662005081 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; cl01054 420662005082 dimerization interface [polypeptide binding]; other site 420662005083 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662005084 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662005085 dimer interface [polypeptide binding]; other site 420662005086 putative CheW interface [polypeptide binding]; other site 420662005087 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]; Region: COG2846 420662005088 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 420662005089 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 420662005090 NnrS protein; Region: NnrS; pfam05940 420662005091 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 420662005092 active site clefts [active] 420662005093 zinc binding site [ion binding]; other site 420662005094 dimer interface [polypeptide binding]; other site 420662005095 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 420662005096 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 420662005097 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 420662005098 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 420662005099 4Fe-4S binding domain; Region: Fer4; cl02805 420662005100 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; cl00470 420662005101 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 420662005102 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 420662005103 [4Fe-4S] binding site [ion binding]; other site 420662005104 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 420662005105 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 420662005106 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 420662005107 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 420662005108 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 420662005109 molybdopterin cofactor binding site; other site 420662005110 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 420662005111 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 420662005112 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 420662005113 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 420662005114 putative substrate translocation pore; other site 420662005115 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 420662005116 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662005117 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662005118 Predicted integral membrane protein [Function unknown]; Region: COG5615 420662005119 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 420662005120 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 420662005121 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 420662005122 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 420662005123 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 420662005124 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662005125 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 420662005126 dimerization interface [polypeptide binding]; other site 420662005127 tellurium resistance terB-like protein; Region: terB_like; cl11965 420662005128 metal binding site [ion binding]; metal-binding site 420662005129 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 420662005130 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662005131 active site 420662005132 metal binding site [ion binding]; metal-binding site 420662005133 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 420662005134 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 420662005135 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 420662005136 Protein of unknown function (DUF3616); Region: DUF3616; pfam12275 420662005137 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 420662005138 YccA-like proteins; Region: YccA_like; cd10433 420662005139 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 420662005140 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 420662005141 active site 420662005142 DNA binding site [nucleotide binding] 420662005143 Int/Topo IB signature motif; other site 420662005144 DJ-1 family protein; Region: not_thiJ; TIGR01383 420662005145 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 420662005146 conserved cys residue [active] 420662005147 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 420662005148 FAD binding domain; Region: FAD_binding_3; pfam01494 420662005149 hypothetical protein; Provisional; Region: PRK07236 420662005150 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 420662005151 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 420662005152 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 420662005153 DNA binding site [nucleotide binding] 420662005154 AAA ATPase domain; Region: AAA_16; pfam13191 420662005155 ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to...; Region: ASCH_Ef3133_like; cd06553 420662005156 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 420662005157 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 420662005158 N-terminal plug; other site 420662005159 ligand-binding site [chemical binding]; other site 420662005160 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 420662005161 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 420662005162 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 420662005163 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 420662005164 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 420662005165 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 420662005166 active site 420662005167 phosphorylation site [posttranslational modification] 420662005168 intermolecular recognition site; other site 420662005169 dimerization interface [polypeptide binding]; other site 420662005170 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662005171 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662005172 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 420662005173 ATP binding site [chemical binding]; other site 420662005174 Mg2+ binding site [ion binding]; other site 420662005175 G-X-G motif; other site 420662005176 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 420662005177 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 420662005178 Subunit I/III interface [polypeptide binding]; other site 420662005179 Subunit III/IV interface [polypeptide binding]; other site 420662005180 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 420662005181 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 420662005182 D-pathway; other site 420662005183 Putative ubiquinol binding site [chemical binding]; other site 420662005184 Low-spin heme (heme b) binding site [chemical binding]; other site 420662005185 Putative water exit pathway; other site 420662005186 Binuclear center (heme o3/CuB) [ion binding]; other site 420662005187 K-pathway; other site 420662005188 Putative proton exit pathway; other site 420662005189 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 420662005190 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 420662005191 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 420662005192 metabolite-proton symporter; Region: 2A0106; TIGR00883 420662005193 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 420662005194 putative substrate translocation pore; other site 420662005195 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 420662005196 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 420662005197 active site 420662005198 catalytic tetrad [active] 420662005199 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 420662005200 nucleoside/Zn binding site; other site 420662005201 dimer interface [polypeptide binding]; other site 420662005202 catalytic motif [active] 420662005203 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 420662005204 dimer interface [polypeptide binding]; other site 420662005205 catalytic triad [active] 420662005206 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_18; cd08505 420662005207 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 420662005208 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 420662005209 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 420662005210 dimer interface [polypeptide binding]; other site 420662005211 conserved gate region; other site 420662005212 putative PBP binding loops; other site 420662005213 ABC-ATPase subunit interface; other site 420662005214 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 420662005215 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 420662005216 dimer interface [polypeptide binding]; other site 420662005217 conserved gate region; other site 420662005218 putative PBP binding loops; other site 420662005219 ABC-ATPase subunit interface; other site 420662005220 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 420662005221 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662005222 Walker A/P-loop; other site 420662005223 ATP binding site [chemical binding]; other site 420662005224 Q-loop/lid; other site 420662005225 ABC transporter signature motif; other site 420662005226 Walker B; other site 420662005227 D-loop; other site 420662005228 H-loop/switch region; other site 420662005229 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 420662005230 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 420662005231 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662005232 Walker A/P-loop; other site 420662005233 ATP binding site [chemical binding]; other site 420662005234 Q-loop/lid; other site 420662005235 ABC transporter signature motif; other site 420662005236 Walker B; other site 420662005237 D-loop; other site 420662005238 H-loop/switch region; other site 420662005239 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 420662005240 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662005241 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 420662005242 N-terminal plug; other site 420662005243 ligand-binding site [chemical binding]; other site 420662005244 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 420662005245 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662005246 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662005247 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662005248 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662005249 Gram-negative bacterial tonB protein; Region: TonB; cl10048 420662005250 PII uridylyl-transferase; Provisional; Region: PRK03059 420662005251 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 420662005252 metal binding triad; other site 420662005253 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 420662005254 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662005255 Zn2+ binding site [ion binding]; other site 420662005256 Mg2+ binding site [ion binding]; other site 420662005257 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 420662005258 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 420662005259 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 420662005260 active site 420662005261 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 420662005262 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 420662005263 dimerization interface [polypeptide binding]; other site 420662005264 ATP binding site [chemical binding]; other site 420662005265 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 420662005266 dimerization interface [polypeptide binding]; other site 420662005267 ATP binding site [chemical binding]; other site 420662005268 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 420662005269 putative active site [active] 420662005270 catalytic triad [active] 420662005271 Protein of unknown function (DUF1624); Region: DUF1624; pfam07786 420662005272 putative transporter; Provisional; Region: PRK10504 420662005273 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 420662005274 putative substrate translocation pore; other site 420662005275 SurA N-terminal domain; Region: SurA_N; pfam09312 420662005276 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 420662005277 BolA-like protein; Region: BolA; pfam01722 420662005278 intracellular septation protein A; Reviewed; Region: PRK00259 420662005279 methionine sulfoxide reductase B; Provisional; Region: PRK00222 420662005280 SelR domain; Region: SelR; pfam01641 420662005281 hypothetical protein; Validated; Region: PRK00029 420662005282 Uncharacterized conserved protein [Function unknown]; Region: COG0397 420662005283 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 420662005284 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 420662005285 dimer interface [polypeptide binding]; other site 420662005286 acyl-activating enzyme (AAE) consensus motif; other site 420662005287 putative active site [active] 420662005288 AMP binding site [chemical binding]; other site 420662005289 putative CoA binding site [chemical binding]; other site 420662005290 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662005291 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 420662005292 putative ligand binding site [chemical binding]; other site 420662005293 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 420662005294 TM-ABC transporter signature motif; other site 420662005295 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 420662005296 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 420662005297 TM-ABC transporter signature motif; other site 420662005298 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 420662005299 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662005300 Walker A/P-loop; other site 420662005301 ATP binding site [chemical binding]; other site 420662005302 Q-loop/lid; other site 420662005303 ABC transporter signature motif; other site 420662005304 Walker B; other site 420662005305 D-loop; other site 420662005306 H-loop/switch region; other site 420662005307 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 420662005308 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662005309 Walker A/P-loop; other site 420662005310 ATP binding site [chemical binding]; other site 420662005311 Q-loop/lid; other site 420662005312 ABC transporter signature motif; other site 420662005313 Walker B; other site 420662005314 D-loop; other site 420662005315 H-loop/switch region; other site 420662005316 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 420662005317 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 420662005318 substrate binding site [chemical binding]; other site 420662005319 oxyanion hole (OAH) forming residues; other site 420662005320 trimer interface [polypeptide binding]; other site 420662005321 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662005322 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662005323 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662005324 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 420662005325 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 420662005326 dimer interface [polypeptide binding]; other site 420662005327 active site 420662005328 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 420662005329 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 420662005330 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 420662005331 active site 420662005332 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 420662005333 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 420662005334 Peptidase M3 Thimet oligopeptidase (TOP) also includes neurolysin; Region: M3A_TOP; cd06455 420662005335 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 420662005336 active site 420662005337 Zn binding site [ion binding]; other site 420662005338 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 420662005339 CoenzymeA binding site [chemical binding]; other site 420662005340 subunit interaction site [polypeptide binding]; other site 420662005341 PHB binding site; other site 420662005342 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 420662005343 Prostaglandin dehydrogenases; Region: PGDH; cd05288 420662005344 NAD(P) binding site [chemical binding]; other site 420662005345 substrate binding site [chemical binding]; other site 420662005346 dimer interface [polypeptide binding]; other site 420662005347 This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine...; Region: Rhizobitoxine-FADS-like; cd03510 420662005348 Fatty acid desaturase; Region: FA_desaturase; pfam00487 420662005349 putative di-iron ligands [ion binding]; other site 420662005350 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 420662005351 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662005352 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 420662005353 C-terminal domain interface [polypeptide binding]; other site 420662005354 GSH binding site (G-site) [chemical binding]; other site 420662005355 dimer interface [polypeptide binding]; other site 420662005356 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 420662005357 N-terminal domain interface [polypeptide binding]; other site 420662005358 hypothetical protein; Provisional; Region: PRK06194 420662005359 classical (c) SDRs; Region: SDR_c; cd05233 420662005360 NAD(P) binding site [chemical binding]; other site 420662005361 active site 420662005362 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 420662005363 biotin synthase; Region: bioB; TIGR00433 420662005364 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 420662005365 FeS/SAM binding site; other site 420662005366 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 420662005367 GYD domain; Region: GYD; pfam08734 420662005368 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 420662005369 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 420662005370 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 420662005371 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 420662005372 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 420662005373 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 420662005374 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 420662005375 RNA binding site [nucleotide binding]; other site 420662005376 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 420662005377 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 420662005378 Ligand binding site; other site 420662005379 DXD motif; other site 420662005380 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 420662005381 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 420662005382 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 420662005383 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 420662005384 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 420662005385 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 420662005386 putative active site [active] 420662005387 metal binding site [ion binding]; metal-binding site 420662005388 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 420662005389 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662005390 substrate binding pocket [chemical binding]; other site 420662005391 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 420662005392 active site 420662005393 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 420662005394 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 420662005395 homotrimer interaction site [polypeptide binding]; other site 420662005396 putative active site [active] 420662005397 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 420662005398 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662005399 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662005400 ABC transporter; Region: ABC_tran_2; pfam12848 420662005401 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662005402 HemK family putative methylases; Region: hemK_fam; TIGR00536 420662005403 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 420662005404 S-adenosylmethionine binding site [chemical binding]; other site 420662005405 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 420662005406 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 420662005407 metal binding site [ion binding]; metal-binding site 420662005408 dimer interface [polypeptide binding]; other site 420662005409 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 420662005410 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 420662005411 ATP binding site [chemical binding]; other site 420662005412 Walker B motif; other site 420662005413 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 420662005414 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 420662005415 active site 420662005416 substrate binding site [chemical binding]; other site 420662005417 trimer interface [polypeptide binding]; other site 420662005418 CoA binding site [chemical binding]; other site 420662005419 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 420662005420 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 420662005421 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662005422 homodimer interface [polypeptide binding]; other site 420662005423 catalytic residue [active] 420662005424 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 420662005425 MarR family; Region: MarR; pfam01047 420662005426 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 420662005427 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 420662005428 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 420662005429 Walker A/P-loop; other site 420662005430 ATP binding site [chemical binding]; other site 420662005431 Q-loop/lid; other site 420662005432 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 420662005433 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 420662005434 Q-loop/lid; other site 420662005435 ABC transporter signature motif; other site 420662005436 Walker B; other site 420662005437 D-loop; other site 420662005438 H-loop/switch region; other site 420662005439 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; cl12038 420662005440 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 420662005441 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 420662005442 nucleotide binding pocket [chemical binding]; other site 420662005443 K-X-D-G motif; other site 420662005444 catalytic site [active] 420662005445 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 420662005446 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 420662005447 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 420662005448 Dimer interface [polypeptide binding]; other site 420662005449 BRCT sequence motif; other site 420662005450 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 420662005451 active site 420662005452 catalytic residues [active] 420662005453 metal binding site [ion binding]; metal-binding site 420662005454 Cupin-like domain; Region: Cupin_8; pfam13621 420662005455 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 420662005456 active site 420662005457 catalytic triad [active] 420662005458 oxyanion hole [active] 420662005459 switch loop; other site 420662005460 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 420662005461 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 420662005462 Walker A/P-loop; other site 420662005463 ATP binding site [chemical binding]; other site 420662005464 Q-loop/lid; other site 420662005465 ABC transporter signature motif; other site 420662005466 Walker B; other site 420662005467 D-loop; other site 420662005468 H-loop/switch region; other site 420662005469 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 420662005470 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 420662005471 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 420662005472 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662005473 active site 420662005474 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 420662005475 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 420662005476 putative substrate translocation pore; other site 420662005477 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 420662005478 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 420662005479 dimerization interface [polypeptide binding]; other site 420662005480 NAD binding site [chemical binding]; other site 420662005481 ligand binding site [chemical binding]; other site 420662005482 catalytic site [active] 420662005483 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 420662005484 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 420662005485 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 420662005486 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 420662005487 active site 420662005488 Protein of unknown function DUF72; Region: DUF72; pfam01904 420662005489 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 420662005490 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 420662005491 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 420662005492 FtsX-like permease family; Region: FtsX; pfam02687 420662005493 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662005494 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 420662005495 Q-loop/lid; other site 420662005496 ABC transporter signature motif; other site 420662005497 Walker B; other site 420662005498 D-loop; other site 420662005499 H-loop/switch region; other site 420662005500 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 420662005501 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 420662005502 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 420662005503 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 420662005504 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 420662005505 [2Fe-2S] cluster binding site [ion binding]; other site 420662005506 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 420662005507 hypothetical protein; Region: PHA01083 420662005508 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 420662005509 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 420662005510 catalytic residue [active] 420662005511 Protein of unknown function (DUF3154); Region: DUF3154; pfam11351 420662005512 SEC-C motif; Region: SEC-C; pfam02810 420662005513 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 420662005514 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 420662005515 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 420662005516 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 420662005517 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 420662005518 active site 420662005519 PilZ domain; Region: PilZ; cl01260 420662005520 DNA polymerase III subunit delta'; Validated; Region: PRK06964 420662005521 DNA polymerase III subunit delta'; Validated; Region: PRK08485 420662005522 thymidylate kinase; Validated; Region: tmk; PRK00698 420662005523 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 420662005524 TMP-binding site; other site 420662005525 ATP-binding site [chemical binding]; other site 420662005526 YceG-like family; Region: YceG; pfam02618 420662005527 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 420662005528 dimerization interface [polypeptide binding]; other site 420662005529 Aminomethyltransferase folate-binding domain; Region: GCV_T; pfam01571 420662005530 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 420662005531 NRDE protein; Region: NRDE; cl01315 420662005532 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 420662005533 active site 420662005534 homodimer interface [polypeptide binding]; other site 420662005535 homotetramer interface [polypeptide binding]; other site 420662005536 LexA repressor; Validated; Region: PRK00215 420662005537 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 420662005538 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 420662005539 Catalytic site [active] 420662005540 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 420662005541 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 420662005542 NAD(P) binding site [chemical binding]; other site 420662005543 homotetramer interface [polypeptide binding]; other site 420662005544 homodimer interface [polypeptide binding]; other site 420662005545 active site 420662005546 putative acyltransferase; Provisional; Region: PRK05790 420662005547 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 420662005548 dimer interface [polypeptide binding]; other site 420662005549 active site 420662005550 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 420662005551 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 420662005552 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 420662005553 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 420662005554 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 420662005555 maleylacetoacetate isomerase; Region: maiA; TIGR01262 420662005556 C-terminal domain interface [polypeptide binding]; other site 420662005557 GSH binding site (G-site) [chemical binding]; other site 420662005558 putative dimer interface [polypeptide binding]; other site 420662005559 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 420662005560 dimer interface [polypeptide binding]; other site 420662005561 N-terminal domain interface [polypeptide binding]; other site 420662005562 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 420662005563 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 420662005564 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 420662005565 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 420662005566 nudix motif; other site 420662005567 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 420662005568 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 420662005569 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662005570 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 420662005571 Walker A/P-loop; other site 420662005572 ATP binding site [chemical binding]; other site 420662005573 Q-loop/lid; other site 420662005574 ABC transporter signature motif; other site 420662005575 Walker B; other site 420662005576 D-loop; other site 420662005577 H-loop/switch region; other site 420662005578 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 420662005579 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 420662005580 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662005581 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 420662005582 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 420662005583 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 420662005584 dimerization interface [polypeptide binding]; other site 420662005585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662005586 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 420662005587 nucleotidyl binding site; other site 420662005588 metal binding site [ion binding]; metal-binding site 420662005589 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 420662005590 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 420662005591 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 420662005592 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 420662005593 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 420662005594 DNA binding residues [nucleotide binding] 420662005595 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 420662005596 IHF dimer interface [polypeptide binding]; other site 420662005597 IHF - DNA interface [nucleotide binding]; other site 420662005598 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 420662005599 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 420662005600 putative tRNA-binding site [nucleotide binding]; other site 420662005601 B3/4 domain; Region: B3_4; pfam03483 420662005602 tRNA synthetase B5 domain; Region: B5; smart00874 420662005603 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 420662005604 dimer interface [polypeptide binding]; other site 420662005605 motif 1; other site 420662005606 motif 3; other site 420662005607 motif 2; other site 420662005608 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 420662005609 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 420662005610 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 420662005611 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 420662005612 dimer interface [polypeptide binding]; other site 420662005613 motif 1; other site 420662005614 active site 420662005615 motif 2; other site 420662005616 motif 3; other site 420662005617 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 420662005618 23S rRNA binding site [nucleotide binding]; other site 420662005619 L21 binding site [polypeptide binding]; other site 420662005620 L13 binding site [polypeptide binding]; other site 420662005621 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 420662005622 translation initiation factor IF-3; Region: infC; TIGR00168 420662005623 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 420662005624 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 420662005625 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 420662005626 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 420662005627 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 420662005628 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 420662005629 active site 420662005630 dimer interface [polypeptide binding]; other site 420662005631 motif 1; other site 420662005632 motif 2; other site 420662005633 motif 3; other site 420662005634 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 420662005635 anticodon binding site; other site 420662005636 isocitrate lyase; Provisional; Region: PRK15063 420662005637 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 420662005638 tetramer interface [polypeptide binding]; other site 420662005639 active site 420662005640 Mg2+/Mn2+ binding site [ion binding]; other site 420662005641 agmatinase; Provisional; Region: PRK02190 420662005642 agmatinase; Region: agmatinase; TIGR01230 420662005643 active site 420662005644 metal binding site [ion binding]; metal-binding site 420662005645 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 420662005646 metal ion-dependent adhesion site (MIDAS); other site 420662005647 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 420662005648 metal ion-dependent adhesion site (MIDAS); other site 420662005649 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 420662005650 Protein of unknown function DUF58; Region: DUF58; pfam01882 420662005651 MoxR-like ATPases [General function prediction only]; Region: COG0714 420662005652 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 420662005653 Walker A motif; other site 420662005654 ATP binding site [chemical binding]; other site 420662005655 Walker B motif; other site 420662005656 arginine finger; other site 420662005657 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662005658 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 420662005659 putative DNA binding site [nucleotide binding]; other site 420662005660 putative Zn2+ binding site [ion binding]; other site 420662005661 AsnC family; Region: AsnC_trans_reg; pfam01037 420662005662 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 420662005663 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 420662005664 inhibitor-cofactor binding pocket; inhibition site 420662005665 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662005666 catalytic residue [active] 420662005667 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 420662005668 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 420662005669 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 420662005670 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 420662005671 catalytic triad [active] 420662005672 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 420662005673 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 420662005674 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 420662005675 putative aminotransferase; Validated; Region: PRK07480 420662005676 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 420662005677 inhibitor-cofactor binding pocket; inhibition site 420662005678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662005679 catalytic residue [active] 420662005680 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 420662005681 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 420662005682 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 420662005683 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662005684 Walker A/P-loop; other site 420662005685 ATP binding site [chemical binding]; other site 420662005686 Q-loop/lid; other site 420662005687 ABC transporter signature motif; other site 420662005688 Walker B; other site 420662005689 D-loop; other site 420662005690 H-loop/switch region; other site 420662005691 TOBE domain; Region: TOBE_2; pfam08402 420662005692 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 420662005693 dimer interface [polypeptide binding]; other site 420662005694 conserved gate region; other site 420662005695 putative PBP binding loops; other site 420662005696 ABC-ATPase subunit interface; other site 420662005697 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 420662005698 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 420662005699 dimer interface [polypeptide binding]; other site 420662005700 conserved gate region; other site 420662005701 putative PBP binding loops; other site 420662005702 ABC-ATPase subunit interface; other site 420662005703 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 420662005704 Protein of unknown function (DUF861); Region: Cupin_3; cl17594 420662005705 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 420662005706 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 420662005707 NAD(P) binding site [chemical binding]; other site 420662005708 catalytic residues [active] 420662005709 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 420662005710 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 420662005711 inhibitor-cofactor binding pocket; inhibition site 420662005712 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662005713 catalytic residue [active] 420662005714 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 420662005715 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 420662005716 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 420662005717 HDOD domain; Region: HDOD; pfam08668 420662005718 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 420662005719 homodimer interface [polypeptide binding]; other site 420662005720 active site 420662005721 UDP-glucose 4-epimerase; Region: PLN02240 420662005722 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 420662005723 NAD binding site [chemical binding]; other site 420662005724 homodimer interface [polypeptide binding]; other site 420662005725 active site 420662005726 substrate binding site [chemical binding]; other site 420662005727 EamA-like transporter family; Region: EamA; pfam00892 420662005728 EamA-like transporter family; Region: EamA; pfam00892 420662005729 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 420662005730 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 420662005731 FMN binding site [chemical binding]; other site 420662005732 active site 420662005733 catalytic residues [active] 420662005734 substrate binding site [chemical binding]; other site 420662005735 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662005736 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 420662005737 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 420662005738 G1 box; other site 420662005739 putative GEF interaction site [polypeptide binding]; other site 420662005740 GTP/Mg2+ binding site [chemical binding]; other site 420662005741 Switch I region; other site 420662005742 G2 box; other site 420662005743 G3 box; other site 420662005744 Switch II region; other site 420662005745 G4 box; other site 420662005746 G5 box; other site 420662005747 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 420662005748 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 420662005749 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 420662005750 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 420662005751 RNA binding site [nucleotide binding]; other site 420662005752 active site 420662005753 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 420662005754 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 420662005755 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 420662005756 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 420662005757 translation initiation factor IF-2; Region: IF-2; TIGR00487 420662005758 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 420662005759 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 420662005760 G1 box; other site 420662005761 putative GEF interaction site [polypeptide binding]; other site 420662005762 GTP/Mg2+ binding site [chemical binding]; other site 420662005763 Switch I region; other site 420662005764 G2 box; other site 420662005765 G3 box; other site 420662005766 Switch II region; other site 420662005767 G4 box; other site 420662005768 G5 box; other site 420662005769 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 420662005770 Translation-initiation factor 2; Region: IF-2; pfam11987 420662005771 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 420662005772 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 420662005773 NusA N-terminal domain; Region: NusA_N; pfam08529 420662005774 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 420662005775 RNA binding site [nucleotide binding]; other site 420662005776 homodimer interface [polypeptide binding]; other site 420662005777 NusA-like KH domain; Region: KH_5; pfam13184 420662005778 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 420662005779 G-X-X-G motif; other site 420662005780 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 420662005781 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 420662005782 ribosome maturation protein RimP; Reviewed; Region: PRK00092 420662005783 Sm and related proteins; Region: Sm_like; cl00259 420662005784 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 420662005785 putative oligomer interface [polypeptide binding]; other site 420662005786 putative RNA binding site [nucleotide binding]; other site 420662005787 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 420662005788 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 420662005789 NAD binding site [chemical binding]; other site 420662005790 homotetramer interface [polypeptide binding]; other site 420662005791 homodimer interface [polypeptide binding]; other site 420662005792 substrate binding site [chemical binding]; other site 420662005793 active site 420662005794 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 420662005795 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 420662005796 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 420662005797 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662005798 catalytic residue [active] 420662005799 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 420662005800 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 420662005801 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 420662005802 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 420662005803 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 420662005804 NAD(P) binding site [chemical binding]; other site 420662005805 Afadin- and alpha -actinin-Binding; Region: ADIP; pfam11559 420662005806 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 420662005807 Beta protein; Region: Beta_protein; pfam14350 420662005808 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 420662005809 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 420662005810 dimerization interface [polypeptide binding]; other site 420662005811 ligand binding site [chemical binding]; other site 420662005812 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 420662005813 multifunctional aminopeptidase A; Provisional; Region: PRK00913 420662005814 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 420662005815 interface (dimer of trimers) [polypeptide binding]; other site 420662005816 Substrate-binding/catalytic site; other site 420662005817 Zn-binding sites [ion binding]; other site 420662005818 Predicted permeases [General function prediction only]; Region: COG0795 420662005819 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 420662005820 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 420662005821 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 420662005822 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 420662005823 putative active site [active] 420662005824 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 420662005825 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662005826 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 420662005827 substrate binding site [chemical binding]; other site 420662005828 dimerization interface [polypeptide binding]; other site 420662005829 methionine aminotransferase; Validated; Region: PRK09082 420662005830 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 420662005831 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662005832 homodimer interface [polypeptide binding]; other site 420662005833 catalytic residue [active] 420662005834 enoyl-CoA hydratase; Provisional; Region: PRK07511 420662005835 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 420662005836 substrate binding site [chemical binding]; other site 420662005837 oxyanion hole (OAH) forming residues; other site 420662005838 trimer interface [polypeptide binding]; other site 420662005839 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 420662005840 catalytic core [active] 420662005841 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662005842 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 420662005843 ligand binding site [chemical binding]; other site 420662005844 flexible hinge region; other site 420662005845 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; cl17320 420662005846 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 420662005847 putative active site [active] 420662005848 putative substrate binding site [chemical binding]; other site 420662005849 ATP binding site [chemical binding]; other site 420662005850 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 420662005851 Acyl-CoA dehydrogenases similar to fadE2; Region: ACAD_FadE2; cd01155 420662005852 FAD binding site [chemical binding]; other site 420662005853 substrate binding site [chemical binding]; other site 420662005854 catalytic base [active] 420662005855 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 420662005856 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 420662005857 C-terminal domain interface [polypeptide binding]; other site 420662005858 GSH binding site (G-site) [chemical binding]; other site 420662005859 dimer interface [polypeptide binding]; other site 420662005860 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 420662005861 N-terminal domain interface [polypeptide binding]; other site 420662005862 putative dimer interface [polypeptide binding]; other site 420662005863 active site 420662005864 SurA N-terminal domain; Region: SurA_N_3; cl07813 420662005865 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 420662005866 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 420662005867 IHF dimer interface [polypeptide binding]; other site 420662005868 IHF - DNA interface [nucleotide binding]; other site 420662005869 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662005870 EamA-like transporter family; Region: EamA; pfam00892 420662005871 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 420662005872 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 420662005873 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 420662005874 GIY-YIG motif/motif A; other site 420662005875 active site 420662005876 catalytic site [active] 420662005877 putative DNA binding site [nucleotide binding]; other site 420662005878 metal binding site [ion binding]; metal-binding site 420662005879 UvrB/uvrC motif; Region: UVR; pfam02151 420662005880 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 420662005881 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 420662005882 conserved hypothetical protein, PP_1857 family; Region: efp_adjacent_2; TIGR03837 420662005883 elongation factor P; Validated; Region: PRK00529 420662005884 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 420662005885 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 420662005886 RNA binding site [nucleotide binding]; other site 420662005887 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 420662005888 RNA binding site [nucleotide binding]; other site 420662005889 Protein of unknown function (DUF3445); Region: DUF3445; pfam11927 420662005890 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 420662005891 Uncharacterized conserved protein [Function unknown]; Region: COG4121 420662005892 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 420662005893 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 420662005894 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 420662005895 RNA/DNA hybrid binding site [nucleotide binding]; other site 420662005896 active site 420662005897 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 420662005898 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 420662005899 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 420662005900 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 420662005901 active site 420662005902 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 420662005903 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 420662005904 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 420662005905 trimer interface [polypeptide binding]; other site 420662005906 active site 420662005907 UDP-GlcNAc binding site [chemical binding]; other site 420662005908 lipid binding site [chemical binding]; lipid-binding site 420662005909 periplasmic chaperone; Provisional; Region: PRK10780 420662005910 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 420662005911 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 420662005912 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662005913 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662005914 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662005915 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 420662005916 Surface antigen; Region: Bac_surface_Ag; pfam01103 420662005917 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 420662005918 zinc metallopeptidase RseP; Provisional; Region: PRK10779 420662005919 active site 420662005920 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 420662005921 protein binding site [polypeptide binding]; other site 420662005922 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 420662005923 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 420662005924 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 420662005925 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 420662005926 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 420662005927 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 420662005928 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 420662005929 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 420662005930 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 420662005931 catalytic residue [active] 420662005932 putative FPP diphosphate binding site; other site 420662005933 putative FPP binding hydrophobic cleft; other site 420662005934 dimer interface [polypeptide binding]; other site 420662005935 putative IPP diphosphate binding site; other site 420662005936 ribosome recycling factor; Reviewed; Region: frr; PRK00083 420662005937 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 420662005938 hinge region; other site 420662005939 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 420662005940 putative nucleotide binding site [chemical binding]; other site 420662005941 uridine monophosphate binding site [chemical binding]; other site 420662005942 homohexameric interface [polypeptide binding]; other site 420662005943 elongation factor Ts; Provisional; Region: tsf; PRK09377 420662005944 UBA/TS-N domain; Region: UBA; pfam00627 420662005945 Elongation factor TS; Region: EF_TS; pfam00889 420662005946 Elongation factor TS; Region: EF_TS; pfam00889 420662005947 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 420662005948 rRNA interaction site [nucleotide binding]; other site 420662005949 S8 interaction site; other site 420662005950 amidase; Provisional; Region: PRK07056 420662005951 Amidase; Region: Amidase; cl11426 420662005952 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 420662005953 putative carbohydrate kinase; Provisional; Region: PRK10565 420662005954 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 420662005955 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 420662005956 putative substrate binding site [chemical binding]; other site 420662005957 putative ATP binding site [chemical binding]; other site 420662005958 ribonuclease R; Region: RNase_R; TIGR02063 420662005959 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 420662005960 RNB domain; Region: RNB; pfam00773 420662005961 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 420662005962 RNA binding site [nucleotide binding]; other site 420662005963 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662005964 active site 420662005965 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 420662005966 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 420662005967 GDP-binding site [chemical binding]; other site 420662005968 ACT binding site; other site 420662005969 IMP binding site; other site 420662005970 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 420662005971 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 420662005972 dimer interface [polypeptide binding]; other site 420662005973 motif 1; other site 420662005974 active site 420662005975 motif 2; other site 420662005976 motif 3; other site 420662005977 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 420662005978 HflC protein; Region: hflC; TIGR01932 420662005979 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 420662005980 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 420662005981 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 420662005982 HflK protein; Region: hflK; TIGR01933 420662005983 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 420662005984 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 420662005985 HflX GTPase family; Region: HflX; cd01878 420662005986 G1 box; other site 420662005987 GTP/Mg2+ binding site [chemical binding]; other site 420662005988 Switch I region; other site 420662005989 G2 box; other site 420662005990 G3 box; other site 420662005991 Switch II region; other site 420662005992 G4 box; other site 420662005993 G5 box; other site 420662005994 bacterial Hfq-like; Region: Hfq; cd01716 420662005995 hexamer interface [polypeptide binding]; other site 420662005996 Sm1 motif; other site 420662005997 RNA binding site [nucleotide binding]; other site 420662005998 Sm2 motif; other site 420662005999 GTP-binding protein Der; Reviewed; Region: PRK00093 420662006000 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 420662006001 G1 box; other site 420662006002 GTP/Mg2+ binding site [chemical binding]; other site 420662006003 Switch I region; other site 420662006004 G2 box; other site 420662006005 Switch II region; other site 420662006006 G3 box; other site 420662006007 G4 box; other site 420662006008 G5 box; other site 420662006009 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 420662006010 G1 box; other site 420662006011 GTP/Mg2+ binding site [chemical binding]; other site 420662006012 Switch I region; other site 420662006013 G2 box; other site 420662006014 G3 box; other site 420662006015 Switch II region; other site 420662006016 G4 box; other site 420662006017 G5 box; other site 420662006018 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 420662006019 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 420662006020 Trp docking motif [polypeptide binding]; other site 420662006021 active site 420662006022 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 420662006023 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 420662006024 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 420662006025 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 420662006026 dimer interface [polypeptide binding]; other site 420662006027 motif 1; other site 420662006028 active site 420662006029 motif 2; other site 420662006030 motif 3; other site 420662006031 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 420662006032 anticodon binding site; other site 420662006033 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 420662006034 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 420662006035 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 420662006036 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 420662006037 non-specific DNA binding site [nucleotide binding]; other site 420662006038 salt bridge; other site 420662006039 sequence-specific DNA binding site [nucleotide binding]; other site 420662006040 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 420662006041 TPR repeat; Region: TPR_11; pfam13414 420662006042 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 420662006043 binding surface 420662006044 TPR motif; other site 420662006045 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 420662006046 TPR motif; other site 420662006047 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 420662006048 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 420662006049 FeS/SAM binding site; other site 420662006050 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 420662006051 active site 420662006052 multimer interface [polypeptide binding]; other site 420662006053 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 420662006054 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 420662006055 RNA binding surface [nucleotide binding]; other site 420662006056 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 420662006057 probable active site [active] 420662006058 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 420662006059 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 420662006060 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 420662006061 RNA binding surface [nucleotide binding]; other site 420662006062 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 420662006063 active site 420662006064 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 420662006065 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 420662006066 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 420662006067 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 420662006068 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 420662006069 active site 420662006070 Predicted ATPase [General function prediction only]; Region: COG1485 420662006071 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 420662006072 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662006073 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 420662006074 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 420662006075 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 420662006076 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 420662006077 E3 interaction surface; other site 420662006078 lipoyl attachment site [posttranslational modification]; other site 420662006079 e3 binding domain; Region: E3_binding; pfam02817 420662006080 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 420662006081 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 420662006082 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 420662006083 TPP-binding site [chemical binding]; other site 420662006084 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 420662006085 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 420662006086 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 420662006087 dimerization interface [polypeptide binding]; other site 420662006088 domain crossover interface; other site 420662006089 redox-dependent activation switch; other site 420662006090 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 420662006091 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 420662006092 trimer interface [polypeptide binding]; other site 420662006093 putative metal binding site [ion binding]; other site 420662006094 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662006095 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 420662006096 dinuclear metal binding motif [ion binding]; other site 420662006097 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 420662006098 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; cl00474 420662006099 active site 420662006100 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 420662006101 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 420662006102 active site 420662006103 Int/Topo IB signature motif; other site 420662006104 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662006105 Predicted permeases [General function prediction only]; Region: COG0679 420662006106 epoxyqueuosine reductase; Region: TIGR00276 420662006107 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 420662006108 4Fe-4S binding domain; Region: Fer4; cl02805 420662006109 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 420662006110 AMIN domain; Region: AMIN; pfam11741 420662006111 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 420662006112 active site 420662006113 metal binding site [ion binding]; metal-binding site 420662006114 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 420662006115 DNA-binding site [nucleotide binding]; DNA binding site 420662006116 RNA-binding motif; other site 420662006117 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 420662006118 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 420662006119 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 420662006120 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 420662006121 TrkA-N domain; Region: TrkA_N; pfam02254 420662006122 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 420662006123 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 420662006124 ATP binding site [chemical binding]; other site 420662006125 Mg2+ binding site [ion binding]; other site 420662006126 G-X-G motif; other site 420662006127 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 420662006128 ATP binding site [chemical binding]; other site 420662006129 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 420662006130 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 420662006131 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 420662006132 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 420662006133 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 420662006134 RNA binding surface [nucleotide binding]; other site 420662006135 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 420662006136 active site 420662006137 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 420662006138 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 420662006139 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 420662006140 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 420662006141 Walker A/P-loop; other site 420662006142 ATP binding site [chemical binding]; other site 420662006143 Q-loop/lid; other site 420662006144 ABC transporter signature motif; other site 420662006145 Walker B; other site 420662006146 D-loop; other site 420662006147 H-loop/switch region; other site 420662006148 AzlC protein; Region: AzlC; pfam03591 420662006149 Predicted membrane protein [Function unknown]; Region: COG4541 420662006150 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 420662006151 Transcriptional regulator [Transcription]; Region: PaiB; COG2808 420662006152 Putative amidotransferase; Region: DUF4066; pfam13278 420662006153 conserved cys residue [active] 420662006154 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 420662006155 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662006156 DNA-binding site [nucleotide binding]; DNA binding site 420662006157 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 420662006158 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662006159 homodimer interface [polypeptide binding]; other site 420662006160 catalytic residue [active] 420662006161 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 420662006162 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 420662006163 putative dimer interface [polypeptide binding]; other site 420662006164 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 420662006165 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 420662006166 putative dimer interface [polypeptide binding]; other site 420662006167 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 420662006168 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 420662006169 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 420662006170 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 420662006171 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 420662006172 FtsX-like permease family; Region: FtsX; pfam02687 420662006173 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 420662006174 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 420662006175 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662006176 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 420662006177 Walker A/P-loop; other site 420662006178 ATP binding site [chemical binding]; other site 420662006179 Q-loop/lid; other site 420662006180 ABC transporter signature motif; other site 420662006181 Walker B; other site 420662006182 D-loop; other site 420662006183 H-loop/switch region; other site 420662006184 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 420662006185 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662006186 ligand binding site [chemical binding]; other site 420662006187 thymidylate synthase; Reviewed; Region: thyA; PRK01827 420662006188 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 420662006189 dimerization interface [polypeptide binding]; other site 420662006190 active site 420662006191 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 420662006192 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 420662006193 folate binding site [chemical binding]; other site 420662006194 NADP+ binding site [chemical binding]; other site 420662006195 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; pfam10013 420662006196 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 420662006197 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 420662006198 DNA photolyase; Region: DNA_photolyase; pfam00875 420662006199 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 420662006200 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 420662006201 putative dimer interface [polypeptide binding]; other site 420662006202 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 420662006203 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 420662006204 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 420662006205 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 420662006206 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 420662006207 Walker A motif; other site 420662006208 ATP binding site [chemical binding]; other site 420662006209 Walker B motif; other site 420662006210 arginine finger; other site 420662006211 Peptidase family M41; Region: Peptidase_M41; pfam01434 420662006212 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 420662006213 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 420662006214 tetramer interface [polypeptide binding]; other site 420662006215 catalytic Zn binding site [ion binding]; other site 420662006216 NADP binding site [chemical binding]; other site 420662006217 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 420662006218 CoA binding domain; Region: CoA_binding_2; pfam13380 420662006219 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 420662006220 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 420662006221 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 420662006222 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 420662006223 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 420662006224 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 420662006225 AAA domain; Region: AAA_33; pfam13671 420662006226 ATP-binding site [chemical binding]; other site 420662006227 Gluconate-6-phosphate binding site [chemical binding]; other site 420662006228 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 420662006229 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 420662006230 Walker A/P-loop; other site 420662006231 ATP binding site [chemical binding]; other site 420662006232 Q-loop/lid; other site 420662006233 ABC transporter signature motif; other site 420662006234 Walker B; other site 420662006235 D-loop; other site 420662006236 H-loop/switch region; other site 420662006237 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 420662006238 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662006239 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662006240 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 420662006241 putative catalytic site [active] 420662006242 putative phosphate binding site [ion binding]; other site 420662006243 active site 420662006244 metal binding site A [ion binding]; metal-binding site 420662006245 DNA binding site [nucleotide binding] 420662006246 putative AP binding site [nucleotide binding]; other site 420662006247 putative metal binding site B [ion binding]; other site 420662006248 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 420662006249 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 420662006250 Response regulator receiver domain; Region: Response_reg; pfam00072 420662006251 active site 420662006252 phosphorylation site [posttranslational modification] 420662006253 intermolecular recognition site; other site 420662006254 dimerization interface [polypeptide binding]; other site 420662006255 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 420662006256 Walker A motif; other site 420662006257 ATP binding site [chemical binding]; other site 420662006258 Walker B motif; other site 420662006259 arginine finger; other site 420662006260 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662006261 PAS domain; Region: PAS; smart00091 420662006262 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 420662006263 putative active site [active] 420662006264 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 420662006265 dimer interface [polypeptide binding]; other site 420662006266 phosphorylation site [posttranslational modification] 420662006267 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 420662006268 ATP binding site [chemical binding]; other site 420662006269 Mg2+ binding site [ion binding]; other site 420662006270 G-X-G motif; other site 420662006271 glutamine synthetase; Provisional; Region: glnA; PRK09469 420662006272 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 420662006273 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 420662006274 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 420662006275 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 420662006276 putative MPT binding site; other site 420662006277 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 420662006278 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 420662006279 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 420662006280 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 420662006281 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 420662006282 NodB motif; other site 420662006283 active site 420662006284 catalytic site [active] 420662006285 metal binding site [ion binding]; metal-binding site 420662006286 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 420662006287 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 420662006288 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 420662006289 fructokinase; Reviewed; Region: PRK09557 420662006290 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 420662006291 nucleotide binding site [chemical binding]; other site 420662006292 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 420662006293 active site 420662006294 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 420662006295 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662006296 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662006297 ABC transporter; Region: ABC_tran_2; pfam12848 420662006298 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 420662006299 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 420662006300 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 420662006301 bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a...; Region: bact_SoxC_Moco; cd02113 420662006302 Moco binding site; other site 420662006303 metal coordination site [ion binding]; other site 420662006304 dimerization interface [polypeptide binding]; other site 420662006305 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 420662006306 DEAD-like helicases superfamily; Region: DEXDc; smart00487 420662006307 ATP binding site [chemical binding]; other site 420662006308 Mg++ binding site [ion binding]; other site 420662006309 motif III; other site 420662006310 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 420662006311 nucleotide binding region [chemical binding]; other site 420662006312 ATP-binding site [chemical binding]; other site 420662006313 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 420662006314 hypothetical protein; Validated; Region: PRK02101 420662006315 hypothetical protein; Provisional; Region: PRK01842 420662006316 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 420662006317 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 420662006318 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 420662006319 catalytic residue [active] 420662006320 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 420662006321 catalytic residues [active] 420662006322 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662006323 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662006324 peroxiredoxin; Region: AhpC; TIGR03137 420662006325 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 420662006326 dimer interface [polypeptide binding]; other site 420662006327 decamer (pentamer of dimers) interface [polypeptide binding]; other site 420662006328 catalytic triad [active] 420662006329 peroxidatic and resolving cysteines [active] 420662006330 Protein of unknown function (DUF3501); Region: DUF3501; pfam12007 420662006331 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 420662006332 Cysteine-rich domain; Region: CCG; pfam02754 420662006333 Cysteine-rich domain; Region: CCG; pfam02754 420662006334 Rubrerythrin [Energy production and conversion]; Region: COG1592 420662006335 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 420662006336 binuclear metal center [ion binding]; other site 420662006337 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 420662006338 Transcriptional regulator [Transcription]; Region: IclR; COG1414 420662006339 Bacterial transcriptional regulator; Region: IclR; pfam01614 420662006340 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 420662006341 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 420662006342 2-isopropylmalate synthase; Validated; Region: PRK00915 420662006343 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 420662006344 active site 420662006345 catalytic residues [active] 420662006346 metal binding site [ion binding]; metal-binding site 420662006347 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 420662006348 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 420662006349 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 420662006350 ketol-acid reductoisomerase; Provisional; Region: PRK05479 420662006351 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 420662006352 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 420662006353 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 420662006354 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 420662006355 putative valine binding site [chemical binding]; other site 420662006356 dimer interface [polypeptide binding]; other site 420662006357 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 420662006358 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 420662006359 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 420662006360 PYR/PP interface [polypeptide binding]; other site 420662006361 dimer interface [polypeptide binding]; other site 420662006362 TPP binding site [chemical binding]; other site 420662006363 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 420662006364 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 420662006365 TPP-binding site [chemical binding]; other site 420662006366 dimer interface [polypeptide binding]; other site 420662006367 RNA polymerase factor sigma-70; Validated; Region: PRK09047 420662006368 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 420662006369 DNA binding residues [nucleotide binding] 420662006370 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 420662006371 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 420662006372 RDD family; Region: RDD; cl00746 420662006373 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 420662006374 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 420662006375 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 420662006376 Nitrogen regulatory protein P-II; Region: P-II; smart00938 420662006377 NAD synthetase; Provisional; Region: PRK13981 420662006378 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 420662006379 multimer interface [polypeptide binding]; other site 420662006380 active site 420662006381 catalytic triad [active] 420662006382 protein interface 1 [polypeptide binding]; other site 420662006383 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 420662006384 homodimer interface [polypeptide binding]; other site 420662006385 NAD binding pocket [chemical binding]; other site 420662006386 ATP binding pocket [chemical binding]; other site 420662006387 Mg binding site [ion binding]; other site 420662006388 active-site loop [active] 420662006389 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 420662006390 Protein of unknown function, DUF482; Region: DUF482; pfam04339 420662006391 ornithine--oxo-acid transaminase; Reviewed; Region: rocD; PRK00854 420662006392 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 420662006393 inhibitor-cofactor binding pocket; inhibition site 420662006394 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662006395 catalytic residue [active] 420662006396 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662006397 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 420662006398 AsnC family; Region: AsnC_trans_reg; pfam01037 420662006399 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 420662006400 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662006401 AsnC family; Region: AsnC_trans_reg; pfam01037 420662006402 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 420662006403 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 420662006404 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 420662006405 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 420662006406 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 420662006407 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 420662006408 dimer interface [polypeptide binding]; other site 420662006409 substrate binding site [chemical binding]; other site 420662006410 metal binding sites [ion binding]; metal-binding site 420662006411 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 420662006412 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 420662006413 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662006414 ligand binding site [chemical binding]; other site 420662006415 transcriptional regulator; Provisional; Region: PRK10632 420662006416 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662006417 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 420662006418 putative effector binding pocket; other site 420662006419 dimerization interface [polypeptide binding]; other site 420662006420 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662006421 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 420662006422 C-terminal domain interface [polypeptide binding]; other site 420662006423 GSH binding site (G-site) [chemical binding]; other site 420662006424 dimer interface [polypeptide binding]; other site 420662006425 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 420662006426 N-terminal domain interface [polypeptide binding]; other site 420662006427 dimer interface [polypeptide binding]; other site 420662006428 substrate binding pocket (H-site) [chemical binding]; other site 420662006429 glutathione reductase; Validated; Region: PRK06116 420662006430 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662006431 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662006432 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 420662006433 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 420662006434 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 420662006435 E3 interaction surface; other site 420662006436 lipoyl attachment site [posttranslational modification]; other site 420662006437 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 420662006438 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662006439 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 420662006440 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 420662006441 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 420662006442 E3 interaction surface; other site 420662006443 lipoyl attachment site [posttranslational modification]; other site 420662006444 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 420662006445 E3 interaction surface; other site 420662006446 lipoyl attachment site [posttranslational modification]; other site 420662006447 e3 binding domain; Region: E3_binding; pfam02817 420662006448 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 420662006449 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 420662006450 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 420662006451 dimer interface [polypeptide binding]; other site 420662006452 TPP-binding site [chemical binding]; other site 420662006453 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 420662006454 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 420662006455 putative active site [active] 420662006456 heme pocket [chemical binding]; other site 420662006457 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 420662006458 dimer interface [polypeptide binding]; other site 420662006459 phosphorylation site [posttranslational modification] 420662006460 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 420662006461 ATP binding site [chemical binding]; other site 420662006462 Mg2+ binding site [ion binding]; other site 420662006463 G-X-G motif; other site 420662006464 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 420662006465 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 420662006466 active site 420662006467 phosphorylation site [posttranslational modification] 420662006468 intermolecular recognition site; other site 420662006469 dimerization interface [polypeptide binding]; other site 420662006470 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 420662006471 DNA binding residues [nucleotide binding] 420662006472 dimerization interface [polypeptide binding]; other site 420662006473 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 420662006474 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 420662006475 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 420662006476 homodimer interface [polypeptide binding]; other site 420662006477 NADP binding site [chemical binding]; other site 420662006478 substrate binding site [chemical binding]; other site 420662006479 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 420662006480 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 420662006481 active site 420662006482 Zn binding site [ion binding]; other site 420662006483 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 420662006484 catalytic residues [active] 420662006485 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 420662006486 tetramer (dimer of dimers) interface [polypeptide binding]; other site 420662006487 active site 420662006488 dimer interface [polypeptide binding]; other site 420662006489 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 420662006490 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662006491 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662006492 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 420662006493 Protein export membrane protein; Region: SecD_SecF; cl14618 420662006494 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 420662006495 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 420662006496 quinone interaction residues [chemical binding]; other site 420662006497 active site 420662006498 catalytic residues [active] 420662006499 FMN binding site [chemical binding]; other site 420662006500 substrate binding site [chemical binding]; other site 420662006501 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 420662006502 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 420662006503 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 420662006504 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 420662006505 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 420662006506 active site 420662006507 substrate binding site [chemical binding]; other site 420662006508 metal binding site [ion binding]; metal-binding site 420662006509 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 420662006510 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 420662006511 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 420662006512 DNA binding site [nucleotide binding] 420662006513 active site 420662006514 EamA-like transporter family; Region: EamA; pfam00892 420662006515 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662006516 EamA-like transporter family; Region: EamA; pfam00892 420662006517 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662006518 Microscilla MS158 and related proteins, metallophosphatase domain; Region: MPP_MS158; cd07404 420662006519 putative active site [active] 420662006520 putative metal binding site [ion binding]; other site 420662006521 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 420662006522 Prostaglandin dehydrogenases; Region: PGDH; cd05288 420662006523 NAD(P) binding site [chemical binding]; other site 420662006524 substrate binding site [chemical binding]; other site 420662006525 dimer interface [polypeptide binding]; other site 420662006526 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662006527 FMN reductase, SsuE family; Region: FMN_reduc_SsuE; TIGR03567 420662006528 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 420662006529 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 420662006530 active site 420662006531 KMSKS motif; other site 420662006532 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 420662006533 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 420662006534 homodimer interface [polypeptide binding]; other site 420662006535 substrate-cofactor binding pocket; other site 420662006536 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662006537 catalytic residue [active] 420662006538 amidophosphoribosyltransferase; Provisional; Region: PRK09246 420662006539 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 420662006540 active site 420662006541 tetramer interface [polypeptide binding]; other site 420662006542 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662006543 active site 420662006544 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 420662006545 Colicin V production protein; Region: Colicin_V; pfam02674 420662006546 Sporulation related domain; Region: SPOR; pfam05036 420662006547 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 420662006548 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662006549 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662006550 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 420662006551 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 420662006552 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 420662006553 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 420662006554 substrate binding site [chemical binding]; other site 420662006555 active site 420662006556 catalytic residues [active] 420662006557 heterodimer interface [polypeptide binding]; other site 420662006558 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 420662006559 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 420662006560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662006561 catalytic residue [active] 420662006562 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 420662006563 active site 420662006564 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 420662006565 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 420662006566 dimerization interface 3.5A [polypeptide binding]; other site 420662006567 active site 420662006568 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 420662006569 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 420662006570 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 420662006571 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 420662006572 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 420662006573 tartrate dehydrogenase; Region: TTC; TIGR02089 420662006574 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 420662006575 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 420662006576 substrate binding site [chemical binding]; other site 420662006577 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 420662006578 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 420662006579 substrate binding site [chemical binding]; other site 420662006580 ligand binding site [chemical binding]; other site 420662006581 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 420662006582 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 420662006583 dimer interface [polypeptide binding]; other site 420662006584 active site 420662006585 citrylCoA binding site [chemical binding]; other site 420662006586 NADH binding [chemical binding]; other site 420662006587 cationic pore residues; other site 420662006588 oxalacetate/citrate binding site [chemical binding]; other site 420662006589 coenzyme A binding site [chemical binding]; other site 420662006590 catalytic triad [active] 420662006591 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 420662006592 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 420662006593 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 420662006594 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 420662006595 L-aspartate oxidase; Provisional; Region: PRK06175 420662006596 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 420662006597 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 420662006598 SdhC subunit interface [polypeptide binding]; other site 420662006599 proximal heme binding site [chemical binding]; other site 420662006600 cardiolipin binding site; other site 420662006601 Iron-sulfur protein interface; other site 420662006602 proximal quinone binding site [chemical binding]; other site 420662006603 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 420662006604 Iron-sulfur protein interface; other site 420662006605 proximal quinone binding site [chemical binding]; other site 420662006606 SdhD (CybS) interface [polypeptide binding]; other site 420662006607 proximal heme binding site [chemical binding]; other site 420662006608 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 420662006609 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662006610 DNA-binding site [nucleotide binding]; DNA binding site 420662006611 UTRA domain; Region: UTRA; pfam07702 420662006612 malate dehydrogenase; Provisional; Region: PRK05442 420662006613 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 420662006614 NAD(P) binding site [chemical binding]; other site 420662006615 dimer interface [polypeptide binding]; other site 420662006616 malate binding site [chemical binding]; other site 420662006617 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 420662006618 BON domain; Region: BON; pfam04972 420662006619 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 420662006620 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 420662006621 ATP binding site [chemical binding]; other site 420662006622 Mg++ binding site [ion binding]; other site 420662006623 motif III; other site 420662006624 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 420662006625 nucleotide binding region [chemical binding]; other site 420662006626 ATP-binding site [chemical binding]; other site 420662006627 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 420662006628 putative RNA binding site [nucleotide binding]; other site 420662006629 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 420662006630 Domain of unknown function (DUF4397); Region: DUF4397; pfam14344 420662006631 Domain of unknown function (DUF4397); Region: DUF4397; pfam14344 420662006632 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 420662006633 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 420662006634 active site 420662006635 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 420662006636 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662006637 active site 420662006638 metal binding site [ion binding]; metal-binding site 420662006639 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 420662006640 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 420662006641 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 420662006642 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662006643 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 420662006644 Walker A/P-loop; other site 420662006645 ATP binding site [chemical binding]; other site 420662006646 Q-loop/lid; other site 420662006647 ABC transporter signature motif; other site 420662006648 Walker B; other site 420662006649 D-loop; other site 420662006650 H-loop/switch region; other site 420662006651 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 420662006652 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 420662006653 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 420662006654 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 420662006655 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 420662006656 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 420662006657 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 420662006658 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 420662006659 Prolyl oligopeptidase, N-terminal beta-propeller domain; Region: Peptidase_S9_N; pfam02897 420662006660 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 420662006661 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 420662006662 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 420662006663 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 420662006664 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 420662006665 active site 420662006666 High potential iron-sulfur protein; Region: HIPIP; pfam01355 420662006667 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 420662006668 RNA binding surface [nucleotide binding]; other site 420662006669 selenophosphate synthetase; Provisional; Region: PRK00943 420662006670 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 420662006671 dimerization interface [polypeptide binding]; other site 420662006672 putative ATP binding site [chemical binding]; other site 420662006673 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 420662006674 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; cl00125 420662006675 active site residue [active] 420662006676 Sensors of blue-light using FAD; Region: BLUF; smart01034 420662006677 transcriptional regulator FixK; Provisional; Region: fixK; PRK09391 420662006678 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 420662006679 ligand binding site [chemical binding]; other site 420662006680 flexible hinge region; other site 420662006681 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 420662006682 putative switch regulator; other site 420662006683 non-specific DNA interactions [nucleotide binding]; other site 420662006684 DNA binding site [nucleotide binding] 420662006685 sequence specific DNA binding site [nucleotide binding]; other site 420662006686 putative cAMP binding site [chemical binding]; other site 420662006687 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 420662006688 DNA-binding site [nucleotide binding]; DNA binding site 420662006689 RNA-binding motif; other site 420662006690 putative chaperone; Provisional; Region: PRK11678 420662006691 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 420662006692 nucleotide binding site [chemical binding]; other site 420662006693 putative NEF/HSP70 interaction site [polypeptide binding]; other site 420662006694 SBD interface [polypeptide binding]; other site 420662006695 Chromate transporter; Region: Chromate_transp; pfam02417 420662006696 Chromate transporter; Region: Chromate_transp; pfam02417 420662006697 Predicted acetyltransferase [General function prediction only]; Region: COG2388 420662006698 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 420662006699 trimer interface [polypeptide binding]; other site 420662006700 putative Zn binding site [ion binding]; other site 420662006701 glycolate transporter; Provisional; Region: PRK09695 420662006702 L-lactate permease; Region: Lactate_perm; cl00701 420662006703 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 420662006704 active site 420662006705 catalytic site [active] 420662006706 substrate binding site [chemical binding]; other site 420662006707 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 420662006708 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 420662006709 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 420662006710 PAS domain S-box; Region: sensory_box; TIGR00229 420662006711 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 420662006712 putative active site [active] 420662006713 heme pocket [chemical binding]; other site 420662006714 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662006715 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662006716 metal binding site [ion binding]; metal-binding site 420662006717 active site 420662006718 I-site; other site 420662006719 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 420662006720 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 420662006721 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 420662006722 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662006723 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 420662006724 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 420662006725 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 420662006726 active site 420662006727 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 420662006728 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662006729 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662006730 metal binding site [ion binding]; metal-binding site 420662006731 active site 420662006732 I-site; other site 420662006733 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 420662006734 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional; Region: PRK03537 420662006735 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 420662006736 PBP superfamily domain; Region: PBP_like_2; pfam12849 420662006737 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 420662006738 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 420662006739 Walker A/P-loop; other site 420662006740 ATP binding site [chemical binding]; other site 420662006741 Q-loop/lid; other site 420662006742 ABC transporter signature motif; other site 420662006743 Walker B; other site 420662006744 D-loop; other site 420662006745 H-loop/switch region; other site 420662006746 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 420662006747 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 420662006748 PBP superfamily domain; Region: PBP_like; pfam12727 420662006749 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 420662006750 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 420662006751 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 420662006752 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 420662006753 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 420662006754 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 420662006755 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 420662006756 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 420662006757 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 420662006758 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 420662006759 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662006760 Subfamily of fatty acid CoA ligase (FACL) similar to Fum10p of Gibberella moniliformis; Region: FACL_fum10p_like; cd05926 420662006761 acyl-activating enzyme (AAE) consensus motif; other site 420662006762 acyl-activating enzyme (AAE) consensus motif; other site 420662006763 putative AMP binding site [chemical binding]; other site 420662006764 putative active site [active] 420662006765 putative CoA binding site [chemical binding]; other site 420662006766 Protein of unknown function (DUF995); Region: DUF995; pfam06191 420662006767 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 420662006768 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 420662006769 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 420662006770 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 420662006771 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 420662006772 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 420662006773 phosphoglycolate phosphatase; Provisional; Region: PRK13222 420662006774 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 420662006775 motif II; other site 420662006776 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 420662006777 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 420662006778 S-adenosylmethionine binding site [chemical binding]; other site 420662006779 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 420662006780 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662006781 ligand binding site [chemical binding]; other site 420662006782 DNA gyrase subunit A; Validated; Region: PRK05560 420662006783 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 420662006784 CAP-like domain; other site 420662006785 active site 420662006786 primary dimer interface [polypeptide binding]; other site 420662006787 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006788 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006789 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006790 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006791 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006792 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 420662006793 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 420662006794 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 420662006795 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662006796 catalytic residue [active] 420662006797 Chorismate mutase type II; Region: CM_2; pfam01817 420662006798 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 420662006799 Prephenate dehydratase; Region: PDT; pfam00800 420662006800 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 420662006801 putative L-Phe binding site [chemical binding]; other site 420662006802 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 420662006803 prephenate dehydrogenase; Validated; Region: PRK08507 420662006804 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 420662006805 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 420662006806 hinge; other site 420662006807 active site 420662006808 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 420662006809 CMP-binding site; other site 420662006810 The sites determining sugar specificity; other site 420662006811 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 420662006812 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 420662006813 RNA binding site [nucleotide binding]; other site 420662006814 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 420662006815 RNA binding site [nucleotide binding]; other site 420662006816 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 420662006817 RNA binding site [nucleotide binding]; other site 420662006818 S1_RPS1_repeat_ec4: 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_ec4; cd05689 420662006819 RNA binding site [nucleotide binding]; other site 420662006820 S1_RPS1_repeat_ec5: 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_ec5; cd05690 420662006821 RNA binding site [nucleotide binding]; other site 420662006822 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 420662006823 RNA binding site [nucleotide binding]; other site 420662006824 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 420662006825 IHF dimer interface [polypeptide binding]; other site 420662006826 IHF - DNA interface [nucleotide binding]; other site 420662006827 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 420662006828 tetratricopeptide repeat protein; Provisional; Region: PRK11788 420662006829 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 420662006830 binding surface 420662006831 TPR motif; other site 420662006832 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 420662006833 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 420662006834 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 420662006835 putative ribose interaction site [chemical binding]; other site 420662006836 putative ADP binding site [chemical binding]; other site 420662006837 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 420662006838 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 420662006839 active site 420662006840 nucleophile elbow; other site 420662006841 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 420662006842 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 420662006843 putative active site [active] 420662006844 putative PHP Thumb interface [polypeptide binding]; other site 420662006845 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 420662006846 generic binding surface II; other site 420662006847 generic binding surface I; other site 420662006848 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 420662006849 LrgA family; Region: LrgA; pfam03788 420662006850 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 420662006851 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 420662006852 active site 420662006853 catalytic site [active] 420662006854 substrate binding site [chemical binding]; other site 420662006855 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 420662006856 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 420662006857 catalytic loop [active] 420662006858 iron binding site [ion binding]; other site 420662006859 chaperone protein HscA; Provisional; Region: hscA; PRK05183 420662006860 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 420662006861 nucleotide binding site [chemical binding]; other site 420662006862 putative NEF/HSP70 interaction site [polypeptide binding]; other site 420662006863 SBD interface [polypeptide binding]; other site 420662006864 co-chaperone HscB; Provisional; Region: hscB; PRK03578 420662006865 DnaJ domain; Region: DnaJ; pfam00226 420662006866 HSP70 interaction site [polypeptide binding]; other site 420662006867 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 420662006868 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 420662006869 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 420662006870 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 420662006871 trimerization site [polypeptide binding]; other site 420662006872 active site 420662006873 cysteine desulfurase; Provisional; Region: PRK14012 420662006874 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 420662006875 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662006876 catalytic residue [active] 420662006877 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 420662006878 Rrf2 family protein; Region: rrf2_super; TIGR00738 420662006879 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 420662006880 Low molecular weight phosphatase family; Region: LMWPc; cd00115 420662006881 active site 420662006882 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 420662006883 active site 1 [active] 420662006884 dimer interface [polypeptide binding]; other site 420662006885 hexamer interface [polypeptide binding]; other site 420662006886 active site 2 [active] 420662006887 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 420662006888 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 420662006889 active site 420662006890 catalytic residues [active] 420662006891 metal binding site [ion binding]; metal-binding site 420662006892 DmpG-like communication domain; Region: DmpG_comm; pfam07836 420662006893 acetaldehyde dehydrogenase; Validated; Region: PRK08300 420662006894 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 420662006895 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 420662006896 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662006897 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662006898 Ycf48-like protein; Provisional; Region: PRK13684 420662006899 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 420662006900 2-oxopent-4-enoate hydratase; Region: catechol_dmpE; TIGR03220 420662006901 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 420662006902 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 420662006903 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 420662006904 NAD binding site [chemical binding]; other site 420662006905 catalytic residues [active] 420662006906 Domain of unknown function (DUF336); Region: DUF336; pfam03928 420662006907 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 420662006908 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 420662006909 active site 420662006910 metal binding site [ion binding]; metal-binding site 420662006911 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 420662006912 tetramer interface [polypeptide binding]; other site 420662006913 active site 420662006914 Fe binding site [ion binding]; other site 420662006915 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662006916 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 420662006917 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662006918 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_Chlorocatechol; cd08446 420662006919 dimerization interface [polypeptide binding]; other site 420662006920 putative substrate binding pocket [chemical binding]; other site 420662006921 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 420662006922 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 420662006923 catalytic loop [active] 420662006924 iron binding site [ion binding]; other site 420662006925 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 420662006926 FAD binding pocket [chemical binding]; other site 420662006927 conserved FAD binding motif [chemical binding]; other site 420662006928 phosphate binding motif [ion binding]; other site 420662006929 beta-alpha-beta structure motif; other site 420662006930 NAD binding pocket [chemical binding]; other site 420662006931 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 420662006932 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 420662006933 dimerization interface [polypeptide binding]; other site 420662006934 putative path to active site cavity [active] 420662006935 diiron center [ion binding]; other site 420662006936 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 420662006937 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 420662006938 dimerization interface [polypeptide binding]; other site 420662006939 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 420662006940 Activator of aromatic catabolism; Region: XylR_N; pfam06505 420662006941 V4R domain; Region: V4R; pfam02830 420662006942 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 420662006943 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 420662006944 Walker A motif; other site 420662006945 ATP binding site [chemical binding]; other site 420662006946 Walker B motif; other site 420662006947 arginine finger; other site 420662006948 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662006949 excinuclease ABC subunit B; Provisional; Region: PRK05298 420662006950 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 420662006951 ATP binding site [chemical binding]; other site 420662006952 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 420662006953 nucleotide binding region [chemical binding]; other site 420662006954 ATP-binding site [chemical binding]; other site 420662006955 Ultra-violet resistance protein B; Region: UvrB; pfam12344 420662006956 UvrB/uvrC motif; Region: UVR; pfam02151 420662006957 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 420662006958 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 420662006959 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 420662006960 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 420662006961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662006962 homodimer interface [polypeptide binding]; other site 420662006963 catalytic residue [active] 420662006964 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 420662006965 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 420662006966 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 420662006967 Putative Fe-S cluster; Region: FeS; cl17515 420662006968 4Fe-4S binding domain; Region: Fer4; cl02805 420662006969 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 420662006970 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 420662006971 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 420662006972 minor groove reading motif; other site 420662006973 helix-hairpin-helix signature motif; other site 420662006974 substrate binding pocket [chemical binding]; other site 420662006975 active site 420662006976 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 420662006977 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4727 420662006978 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 420662006979 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 420662006980 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662006981 putative active site [active] 420662006982 putative metal binding site [ion binding]; other site 420662006983 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 420662006984 cobalamin synthase; Reviewed; Region: cobS; PRK00235 420662006985 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 420662006986 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 420662006987 putative dimer interface [polypeptide binding]; other site 420662006988 active site pocket [active] 420662006989 putative cataytic base [active] 420662006990 cobyric acid synthase; Provisional; Region: PRK00784 420662006991 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 420662006992 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 420662006993 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 420662006994 catalytic triad [active] 420662006995 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 420662006996 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 420662006997 Walker A/P-loop; other site 420662006998 ATP binding site [chemical binding]; other site 420662006999 Q-loop/lid; other site 420662007000 ABC transporter signature motif; other site 420662007001 Walker B; other site 420662007002 D-loop; other site 420662007003 H-loop/switch region; other site 420662007004 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; cl00462 420662007005 FecCD transport family; Region: FecCD; pfam01032 420662007006 putative PBP binding regions; other site 420662007007 ABC-ATPase subunit interface; other site 420662007008 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 420662007009 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 420662007010 intersubunit interface [polypeptide binding]; other site 420662007011 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 420662007012 homotrimer interface [polypeptide binding]; other site 420662007013 Walker A motif; other site 420662007014 GTP binding site [chemical binding]; other site 420662007015 Walker B motif; other site 420662007016 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 420662007017 N-terminal plug; other site 420662007018 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 420662007019 ligand-binding site [chemical binding]; other site 420662007020 Cell division protein ZapA; Region: ZapA; pfam05164 420662007021 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 420662007022 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662007023 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662007024 metal binding site [ion binding]; metal-binding site 420662007025 active site 420662007026 I-site; other site 420662007027 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 420662007028 ANTAR domain; Region: ANTAR; pfam03861 420662007029 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 420662007030 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 420662007031 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 420662007032 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 420662007033 putative substrate translocation pore; other site 420662007034 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 420662007035 Protein phosphatase 2C; Region: PP2C; pfam00481 420662007036 active site 420662007037 Protein kinase domain; Region: Pkinase; pfam00069 420662007038 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662007039 active site 420662007040 ATP binding site [chemical binding]; other site 420662007041 substrate binding site [chemical binding]; other site 420662007042 activation loop (A-loop); other site 420662007043 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662007044 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 420662007045 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662007046 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662007047 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 420662007048 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 420662007049 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 420662007050 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 420662007051 iron-sulfur cluster [ion binding]; other site 420662007052 [2Fe-2S] cluster binding site [ion binding]; other site 420662007053 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 420662007054 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 420662007055 [4Fe-4S] binding site [ion binding]; other site 420662007056 molybdopterin cofactor binding site; other site 420662007057 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 420662007058 molybdopterin cofactor binding site; other site 420662007059 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 420662007060 glycosyl transferase family protein; Provisional; Region: PRK08136 420662007061 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 420662007062 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 420662007063 active site 420662007064 SAM binding site [chemical binding]; other site 420662007065 homodimer interface [polypeptide binding]; other site 420662007066 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 420662007067 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 420662007068 motif 1; other site 420662007069 active site 420662007070 motif 2; other site 420662007071 motif 3; other site 420662007072 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 420662007073 DHHA1 domain; Region: DHHA1; pfam02272 420662007074 succinic semialdehyde dehydrogenase; Region: PLN02278 420662007075 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 420662007076 tetramerization interface [polypeptide binding]; other site 420662007077 NAD(P) binding site [chemical binding]; other site 420662007078 catalytic residues [active] 420662007079 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 420662007080 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662007081 metal binding site [ion binding]; metal-binding site 420662007082 active site 420662007083 I-site; other site 420662007084 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662007085 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662007086 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 420662007087 dimerization interface [polypeptide binding]; other site 420662007088 substrate binding pocket [chemical binding]; other site 420662007089 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662007090 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662007091 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662007092 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 420662007093 dimerization interface [polypeptide binding]; other site 420662007094 substrate binding pocket [chemical binding]; other site 420662007095 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 420662007096 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 420662007097 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 420662007098 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 420662007099 Magnesium ion binding site [ion binding]; other site 420662007100 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 420662007101 ParB-like nuclease domain; Region: ParBc; pfam02195 420662007102 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 420662007103 RES domain; Region: RES; pfam08808 420662007104 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 420662007105 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 420662007106 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 420662007107 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 420662007108 dimer interface [polypeptide binding]; other site 420662007109 ssDNA binding site [nucleotide binding]; other site 420662007110 tetramer (dimer of dimers) interface [polypeptide binding]; other site 420662007111 DNA topoisomerase III; Provisional; Region: PRK07726 420662007112 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 420662007113 active site 420662007114 putative interdomain interaction site [polypeptide binding]; other site 420662007115 putative metal-binding site [ion binding]; other site 420662007116 putative nucleotide binding site [chemical binding]; other site 420662007117 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 420662007118 domain I; other site 420662007119 DNA binding groove [nucleotide binding] 420662007120 phosphate binding site [ion binding]; other site 420662007121 domain II; other site 420662007122 domain III; other site 420662007123 nucleotide binding site [chemical binding]; other site 420662007124 catalytic site [active] 420662007125 domain IV; other site 420662007126 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 420662007127 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 420662007128 ArsC family; Region: ArsC; pfam03960 420662007129 catalytic residues [active] 420662007130 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662007131 Coenzyme A binding pocket [chemical binding]; other site 420662007132 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 420662007133 arsenical-resistance protein; Region: acr3; TIGR00832 420662007134 Low molecular weight phosphatase family; Region: LMWPc; cd00115 420662007135 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 420662007136 active site 420662007137 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 420662007138 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662007139 putative metal binding site [ion binding]; other site 420662007140 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 420662007141 dimerization interface [polypeptide binding]; other site 420662007142 putative DNA binding site [nucleotide binding]; other site 420662007143 putative Zn2+ binding site [ion binding]; other site 420662007144 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 420662007145 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 420662007146 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 420662007147 DNA binding residues [nucleotide binding] 420662007148 dimer interface [polypeptide binding]; other site 420662007149 putative metal binding site [ion binding]; other site 420662007150 Iron permease FTR1 family; Region: FTR1; cl00475 420662007151 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 420662007152 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 420662007153 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 420662007154 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 420662007155 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 420662007156 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 420662007157 MAPEG family; Region: MAPEG; pfam01124 420662007158 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 420662007159 Ca2+ binding site [ion binding]; other site 420662007160 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 420662007161 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 420662007162 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 420662007163 S-adenosylmethionine binding site [chemical binding]; other site 420662007164 DEAD-like helicases superfamily; Region: DEXDc; smart00487 420662007165 Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in...; Region: PTH2_family; cl00869 420662007166 dimer interface [polypeptide binding]; other site 420662007167 putative active site [active] 420662007168 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 420662007169 nucleotide binding region [chemical binding]; other site 420662007170 ATP-binding site [chemical binding]; other site 420662007171 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662007172 ATPase family associated with various cellular activities (AAA); Region: AAA; pfam00004 420662007173 Walker A motif; other site 420662007174 ATP binding site [chemical binding]; other site 420662007175 Walker B motif; other site 420662007176 arginine finger; other site 420662007177 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 420662007178 active site 420662007179 NTP binding site [chemical binding]; other site 420662007180 metal binding triad [ion binding]; metal-binding site 420662007181 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 420662007182 sequence-specific DNA binding site [nucleotide binding]; other site 420662007183 salt bridge; other site 420662007184 Domain of unknown function (DUF955); Region: DUF955; cl01076 420662007185 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 420662007186 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 420662007187 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 420662007188 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 420662007189 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 420662007190 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 420662007191 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 420662007192 PLD-like domain; Region: PLDc_2; pfam13091 420662007193 homodimer interface [polypeptide binding]; other site 420662007194 putative active site [active] 420662007195 catalytic site [active] 420662007196 DNA methylase; Region: N6_N4_Mtase; pfam01555 420662007197 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 420662007198 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 420662007199 S-adenosylmethionine binding site [chemical binding]; other site 420662007200 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 420662007201 DNA methylase; Region: N6_N4_Mtase; pfam01555 420662007202 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 420662007203 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 420662007204 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 420662007205 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 420662007206 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 420662007207 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 420662007208 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 420662007209 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 420662007210 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 420662007211 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 420662007212 Protein of unknown function (DUF904); Region: DUF904; pfam06005 420662007213 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 420662007214 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 420662007215 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 420662007216 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 420662007217 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 420662007218 catalytic residues [active] 420662007219 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 420662007220 MPN+ (JAMM) motif; other site 420662007221 Zinc-binding site [ion binding]; other site 420662007222 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 420662007223 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 420662007224 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 420662007225 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 420662007226 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 420662007227 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 420662007228 Protein of unknwon function (DUF2893); Region: DUF2893; pfam11459 420662007229 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 420662007230 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 420662007231 Putative helicase; Region: TraI_2; pfam07514 420662007232 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 420662007233 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 420662007234 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 420662007235 non-specific DNA binding site [nucleotide binding]; other site 420662007236 salt bridge; other site 420662007237 sequence-specific DNA binding site [nucleotide binding]; other site 420662007238 LysR substrate binding domain; Region: LysR_substrate; pfam03466 420662007239 integrase; Provisional; Region: PRK09692 420662007240 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 420662007241 active site 420662007242 Int/Topo IB signature motif; other site 420662007243 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662007244 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 420662007245 DNA binding residues [nucleotide binding] 420662007246 dimerization interface [polypeptide binding]; other site 420662007247 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662007248 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662007249 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 420662007250 putative effector binding pocket; other site 420662007251 dimerization interface [polypeptide binding]; other site 420662007252 Cupin domain; Region: Cupin_2; cl17218 420662007253 Helix-turn-helix domain; Region: HTH_18; pfam12833 420662007254 ethanolamine permease; Region: 2A0305; TIGR00908 420662007255 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 420662007256 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 420662007257 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 420662007258 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 420662007259 putative hydrophobic ligand binding site [chemical binding]; other site 420662007260 protein interface [polypeptide binding]; other site 420662007261 gate; other site 420662007262 Water Stress and Hypersensitive response; Region: WHy; smart00769 420662007263 Domain of unknown function (DUF1772); Region: DUF1772; cl12097 420662007264 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 420662007265 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 420662007266 S-adenosylmethionine binding site [chemical binding]; other site 420662007267 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 420662007268 dimerization interface [polypeptide binding]; other site 420662007269 putative DNA binding site [nucleotide binding]; other site 420662007270 putative Zn2+ binding site [ion binding]; other site 420662007271 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 420662007272 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662007273 catalytic residues [active] 420662007274 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 420662007275 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 420662007276 Cytochrome c; Region: Cytochrom_C; cl11414 420662007277 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 420662007278 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 420662007279 Domain of unknown function (DUF336); Region: DUF336; pfam03928 420662007280 DsrE/DsrF-like family; Region: DrsE; cl00672 420662007281 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 420662007282 active site 420662007283 metal binding site [ion binding]; metal-binding site 420662007284 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 420662007285 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 420662007286 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 420662007287 Predicted secreted protein [Function unknown]; Region: COG5501 420662007288 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 420662007289 Cytochrome c; Region: Cytochrom_C; pfam00034 420662007290 Cytochrome c; Region: Cytochrom_C; cl11414 420662007291 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 420662007292 Moco binding site; other site 420662007293 metal coordination site [ion binding]; other site 420662007294 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 420662007295 putative DNA binding site [nucleotide binding]; other site 420662007296 putative Zn2+ binding site [ion binding]; other site 420662007297 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 420662007298 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 420662007299 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662007300 DNA-binding site [nucleotide binding]; DNA binding site 420662007301 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 420662007302 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662007303 homodimer interface [polypeptide binding]; other site 420662007304 catalytic residue [active] 420662007305 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662007306 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 420662007307 catalytic site [active] 420662007308 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 420662007309 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662007310 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 420662007311 Transposase domain (DUF772); Region: DUF772; pfam05598 420662007312 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662007313 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662007314 YCII-related domain; Region: YCII; cl00999 420662007315 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662007316 DNA-binding site [nucleotide binding]; DNA binding site 420662007317 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 420662007318 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 420662007319 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662007320 homodimer interface [polypeptide binding]; other site 420662007321 catalytic residue [active] 420662007322 PAS domain; Region: PAS_9; pfam13426 420662007323 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 420662007324 putative active site [active] 420662007325 heme pocket [chemical binding]; other site 420662007326 PAS domain; Region: PAS_9; pfam13426 420662007327 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662007328 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662007329 metal binding site [ion binding]; metal-binding site 420662007330 active site 420662007331 I-site; other site 420662007332 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 420662007333 Response regulator receiver domain; Region: Response_reg; pfam00072 420662007334 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 420662007335 active site 420662007336 phosphorylation site [posttranslational modification] 420662007337 intermolecular recognition site; other site 420662007338 dimerization interface [polypeptide binding]; other site 420662007339 HDOD domain; Region: HDOD; pfam08668 420662007340 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662007341 Zn2+ binding site [ion binding]; other site 420662007342 Mg2+ binding site [ion binding]; other site 420662007343 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 420662007344 ATP binding site [chemical binding]; other site 420662007345 Mg2+ binding site [ion binding]; other site 420662007346 G-X-G motif; other site 420662007347 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 420662007348 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 420662007349 active site 420662007350 phosphorylation site [posttranslational modification] 420662007351 intermolecular recognition site; other site 420662007352 dimerization interface [polypeptide binding]; other site 420662007353 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662007354 Zn2+ binding site [ion binding]; other site 420662007355 Mg2+ binding site [ion binding]; other site 420662007356 Response regulator receiver domain; Region: Response_reg; pfam00072 420662007357 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 420662007358 active site 420662007359 phosphorylation site [posttranslational modification] 420662007360 intermolecular recognition site; other site 420662007361 dimerization interface [polypeptide binding]; other site 420662007362 aspartate kinase; Reviewed; Region: PRK06635 420662007363 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 420662007364 putative nucleotide binding site [chemical binding]; other site 420662007365 putative catalytic residues [active] 420662007366 putative Mg ion binding site [ion binding]; other site 420662007367 putative aspartate binding site [chemical binding]; other site 420662007368 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 420662007369 putative allosteric regulatory site; other site 420662007370 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 420662007371 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 420662007372 Ligand Binding Site [chemical binding]; other site 420662007373 TilS substrate binding domain; Region: TilS; pfam09179 420662007374 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 420662007375 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 420662007376 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 420662007377 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 420662007378 endonuclease III; Region: ENDO3c; smart00478 420662007379 minor groove reading motif; other site 420662007380 helix-hairpin-helix signature motif; other site 420662007381 substrate binding pocket [chemical binding]; other site 420662007382 active site 420662007383 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 420662007384 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 420662007385 active site 420662007386 HIGH motif; other site 420662007387 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 420662007388 KMSKS motif; other site 420662007389 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 420662007390 tRNA binding surface [nucleotide binding]; other site 420662007391 anticodon binding site; other site 420662007392 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 420662007393 substrate binding site [chemical binding]; other site 420662007394 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 420662007395 substrate binding site [chemical binding]; other site 420662007396 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662007397 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 420662007398 putative active site [active] 420662007399 putative metal binding site [ion binding]; other site 420662007400 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 420662007401 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 420662007402 Clp amino terminal domain; Region: Clp_N; pfam02861 420662007403 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 420662007404 Walker A motif; other site 420662007405 ATP binding site [chemical binding]; other site 420662007406 Walker B motif; other site 420662007407 arginine finger; other site 420662007408 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 420662007409 Walker A motif; other site 420662007410 ATP binding site [chemical binding]; other site 420662007411 Walker B motif; other site 420662007412 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 420662007413 ATP-dependent Clp protease adaptor protein ClpS; Reviewed; Region: clpS; PRK00033 420662007414 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 420662007415 DNA-binding site [nucleotide binding]; DNA binding site 420662007416 RNA-binding motif; other site 420662007417 isocitrate dehydrogenase; Validated; Region: PRK07362 420662007418 isocitrate dehydrogenase; Reviewed; Region: PRK07006 420662007419 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 420662007420 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 420662007421 FeS/SAM binding site; other site 420662007422 HemN C-terminal domain; Region: HemN_C; pfam06969 420662007423 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 420662007424 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 420662007425 ligand binding site [chemical binding]; other site 420662007426 flexible hinge region; other site 420662007427 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 420662007428 putative switch regulator; other site 420662007429 non-specific DNA interactions [nucleotide binding]; other site 420662007430 DNA binding site [nucleotide binding] 420662007431 sequence specific DNA binding site [nucleotide binding]; other site 420662007432 putative cAMP binding site [chemical binding]; other site 420662007433 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 420662007434 4Fe-4S binding domain; Region: Fer4_5; pfam12801 420662007435 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 420662007436 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 420662007437 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 420662007438 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662007439 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662007440 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 420662007441 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 420662007442 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 420662007443 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 420662007444 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 420662007445 Low-spin heme binding site [chemical binding]; other site 420662007446 Putative water exit pathway; other site 420662007447 Binuclear center (active site) [active] 420662007448 Putative proton exit pathway; other site 420662007449 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 420662007450 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 420662007451 metal-binding site [ion binding] 420662007452 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 420662007453 Soluble P-type ATPase [General function prediction only]; Region: COG4087 420662007454 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 420662007455 superoxide dismutase; Provisional; Region: PRK10543 420662007456 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 420662007457 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 420662007458 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 420662007459 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 420662007460 generic binding surface II; other site 420662007461 generic binding surface I; other site 420662007462 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 420662007463 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662007464 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 420662007465 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 420662007466 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 420662007467 Uncharacterized conserved protein [Function unknown]; Region: COG2835 420662007468 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 420662007469 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 420662007470 Ligand binding site; other site 420662007471 oligomer interface; other site 420662007472 adenylate kinase; Reviewed; Region: adk; PRK00279 420662007473 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 420662007474 AMP-binding site [chemical binding]; other site 420662007475 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 420662007476 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 420662007477 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 420662007478 NAD binding site [chemical binding]; other site 420662007479 homodimer interface [polypeptide binding]; other site 420662007480 homotetramer interface [polypeptide binding]; other site 420662007481 active site 420662007482 DNA primase, catalytic core; Region: dnaG; TIGR01391 420662007483 CHC2 zinc finger; Region: zf-CHC2; pfam01807 420662007484 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 420662007485 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 420662007486 active site 420662007487 metal binding site [ion binding]; metal-binding site 420662007488 interdomain interaction site; other site 420662007489 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 420662007490 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 420662007491 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 420662007492 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 420662007493 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 420662007494 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662007495 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 420662007496 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 420662007497 DNA binding residues [nucleotide binding] 420662007498 cyclase homology domain; Region: CHD; cd07302 420662007499 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 420662007500 nucleotidyl binding site; other site 420662007501 metal binding site [ion binding]; metal-binding site 420662007502 dimer interface [polypeptide binding]; other site 420662007503 FHA domain; Region: FHA; pfam00498 420662007504 phosphopeptide binding site; other site 420662007505 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 420662007506 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 420662007507 motif II; other site 420662007508 GAF domain; Region: GAF; pfam01590 420662007509 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662007510 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 420662007511 PAS domain; Region: PAS_9; pfam13426 420662007512 putative active site [active] 420662007513 heme pocket [chemical binding]; other site 420662007514 PAS fold; Region: PAS_4; pfam08448 420662007515 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 420662007516 putative active site [active] 420662007517 heme pocket [chemical binding]; other site 420662007518 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 420662007519 PAS domain; Region: PAS_9; pfam13426 420662007520 putative active site [active] 420662007521 heme pocket [chemical binding]; other site 420662007522 PAS domain S-box; Region: sensory_box; TIGR00229 420662007523 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 420662007524 putative active site [active] 420662007525 heme pocket [chemical binding]; other site 420662007526 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 420662007527 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 420662007528 putative active site [active] 420662007529 heme pocket [chemical binding]; other site 420662007530 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 420662007531 dimer interface [polypeptide binding]; other site 420662007532 phosphorylation site [posttranslational modification] 420662007533 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 420662007534 ATP binding site [chemical binding]; other site 420662007535 Mg2+ binding site [ion binding]; other site 420662007536 G-X-G motif; other site 420662007537 Response regulator receiver domain; Region: Response_reg; pfam00072 420662007538 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 420662007539 active site 420662007540 phosphorylation site [posttranslational modification] 420662007541 intermolecular recognition site; other site 420662007542 dimerization interface [polypeptide binding]; other site 420662007543 ferrochelatase; Reviewed; Region: hemH; PRK00035 420662007544 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 420662007545 C-terminal domain interface [polypeptide binding]; other site 420662007546 active site 420662007547 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 420662007548 active site 420662007549 N-terminal domain interface [polypeptide binding]; other site 420662007550 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 420662007551 RNA binding surface [nucleotide binding]; other site 420662007552 GrpE; Region: GrpE; pfam01025 420662007553 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 420662007554 dimer interface [polypeptide binding]; other site 420662007555 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 420662007556 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 420662007557 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 420662007558 nucleotide binding site [chemical binding]; other site 420662007559 chaperone protein DnaJ; Provisional; Region: PRK10767 420662007560 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 420662007561 HSP70 interaction site [polypeptide binding]; other site 420662007562 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 420662007563 Zn binding sites [ion binding]; other site 420662007564 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 420662007565 dimer interface [polypeptide binding]; other site 420662007566 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 420662007567 Sulfatase; Region: Sulfatase; pfam00884 420662007568 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 420662007569 active site 420662007570 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 420662007571 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 420662007572 active site 420662007573 phosphorylation site [posttranslational modification] 420662007574 intermolecular recognition site; other site 420662007575 dimerization interface [polypeptide binding]; other site 420662007576 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 420662007577 DNA binding site [nucleotide binding] 420662007578 sensor protein KdpD; Provisional; Region: PRK10490 420662007579 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 420662007580 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 420662007581 Ligand Binding Site [chemical binding]; other site 420662007582 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 420662007583 GAF domain; Region: GAF_3; pfam13492 420662007584 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 420662007585 dimer interface [polypeptide binding]; other site 420662007586 phosphorylation site [posttranslational modification] 420662007587 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 420662007588 ATP binding site [chemical binding]; other site 420662007589 Mg2+ binding site [ion binding]; other site 420662007590 G-X-G motif; other site 420662007591 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 420662007592 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 420662007593 oligomer interface [polypeptide binding]; other site 420662007594 metal binding site [ion binding]; metal-binding site 420662007595 metal binding site [ion binding]; metal-binding site 420662007596 putative Cl binding site [ion binding]; other site 420662007597 basic sphincter; other site 420662007598 hydrophobic gate; other site 420662007599 periplasmic entrance; other site 420662007600 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 420662007601 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 420662007602 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 420662007603 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 420662007604 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 420662007605 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 420662007606 FeS/SAM binding site; other site 420662007607 PAS fold; Region: PAS_7; pfam12860 420662007608 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 420662007609 putative active site [active] 420662007610 heme pocket [chemical binding]; other site 420662007611 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 420662007612 PAS domain; Region: PAS_9; pfam13426 420662007613 putative active site [active] 420662007614 heme pocket [chemical binding]; other site 420662007615 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662007616 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662007617 metal binding site [ion binding]; metal-binding site 420662007618 active site 420662007619 I-site; other site 420662007620 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 420662007621 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 420662007622 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662007623 Zn2+ binding site [ion binding]; other site 420662007624 Mg2+ binding site [ion binding]; other site 420662007625 LysE type translocator; Region: LysE; cl00565 420662007626 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 420662007627 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662007628 acyl-activating enzyme (AAE) consensus motif; other site 420662007629 AMP binding site [chemical binding]; other site 420662007630 active site 420662007631 CoA binding site [chemical binding]; other site 420662007632 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 420662007633 Isochorismatase family; Region: Isochorismatase; pfam00857 420662007634 catalytic triad [active] 420662007635 dimer interface [polypeptide binding]; other site 420662007636 conserved cis-peptide bond; other site 420662007637 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662007638 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662007639 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2368 420662007640 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 420662007641 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 420662007642 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 420662007643 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 420662007644 NADP binding site [chemical binding]; other site 420662007645 dimer interface [polypeptide binding]; other site 420662007646 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662007647 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662007648 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 420662007649 NlpC/P60 family; Region: NLPC_P60; pfam00877 420662007650 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 420662007651 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 420662007652 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 420662007653 GTP binding site; other site 420662007654 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 420662007655 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662007656 Coenzyme A binding pocket [chemical binding]; other site 420662007657 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 420662007658 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 420662007659 dimer interface [polypeptide binding]; other site 420662007660 putative functional site; other site 420662007661 putative MPT binding site; other site 420662007662 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 420662007663 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662007664 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662007665 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 420662007666 c-type cytochrome, methanol metabolism-related; Region: 4cys_cytochr; TIGR03874 420662007667 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 420662007668 Chromate transporter; Region: Chromate_transp; pfam02417 420662007669 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 420662007670 RNA/DNA hybrid binding site [nucleotide binding]; other site 420662007671 active site 420662007672 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 420662007673 Methyltransferase domain; Region: Methyltransf_11; pfam08241 420662007674 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 420662007675 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 420662007676 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 420662007677 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662007678 catalytic residue [active] 420662007679 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 420662007680 MAPEG family; Region: MAPEG; cl09190 420662007681 recombination protein RecR; Reviewed; Region: recR; PRK00076 420662007682 RecR protein; Region: RecR; pfam02132 420662007683 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 420662007684 putative active site [active] 420662007685 putative metal-binding site [ion binding]; other site 420662007686 tetramer interface [polypeptide binding]; other site 420662007687 hypothetical protein; Validated; Region: PRK00153 420662007688 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14951 420662007689 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 420662007690 Walker A motif; other site 420662007691 ATP binding site [chemical binding]; other site 420662007692 Walker B motif; other site 420662007693 arginine finger; other site 420662007694 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 420662007695 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 420662007696 active site 420662007697 phosphorylation site [posttranslational modification] 420662007698 intermolecular recognition site; other site 420662007699 dimerization interface [polypeptide binding]; other site 420662007700 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 420662007701 DNA binding residues [nucleotide binding] 420662007702 dimerization interface [polypeptide binding]; other site 420662007703 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662007704 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 420662007705 dimer interface [polypeptide binding]; other site 420662007706 phosphorylation site [posttranslational modification] 420662007707 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 420662007708 ATP binding site [chemical binding]; other site 420662007709 Mg2+ binding site [ion binding]; other site 420662007710 G-X-G motif; other site 420662007711 Transposase domain (DUF772); Region: DUF772; pfam05598 420662007712 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662007713 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662007714 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662007715 Toluene-4-monooxygenase system protein B (TmoB); Region: TmoB; pfam06234 420662007716 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 420662007717 [2Fe-2S] cluster binding site [ion binding]; other site 420662007718 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 420662007719 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 420662007720 dimerization interface [polypeptide binding]; other site 420662007721 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662007722 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662007723 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662007724 dimer interface [polypeptide binding]; other site 420662007725 putative CheW interface [polypeptide binding]; other site 420662007726 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 420662007727 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 420662007728 Uncharacterized conserved protein [Function unknown]; Region: COG2308 420662007729 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662007730 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 420662007731 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662007732 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 420662007733 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 420662007734 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 420662007735 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 420662007736 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662007737 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662007738 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 420662007739 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 420662007740 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 420662007741 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 420662007742 Competence protein; Region: Competence; pfam03772 420662007743 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 420662007744 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 420662007745 homotrimer interaction site [polypeptide binding]; other site 420662007746 putative active site [active] 420662007747 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 420662007748 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 420662007749 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 420662007750 CAP-like domain; other site 420662007751 active site 420662007752 primary dimer interface [polypeptide binding]; other site 420662007753 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 420662007754 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; cl00075 420662007755 ATP binding site [chemical binding]; other site 420662007756 Mg2+ binding site [ion binding]; other site 420662007757 G-X-G motif; other site 420662007758 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 420662007759 anchoring element; other site 420662007760 dimer interface [polypeptide binding]; other site 420662007761 ATP binding site [chemical binding]; other site 420662007762 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 420662007763 active site 420662007764 metal binding site [ion binding]; metal-binding site 420662007765 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 420662007766 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 420662007767 putative substrate translocation pore; other site 420662007768 Major Facilitator Superfamily; Region: MFS_1; pfam07690 420662007769 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 420662007770 S-adenosylmethionine binding site [chemical binding]; other site 420662007771 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 420662007772 dihydrodipicolinate synthase; Region: dapA; TIGR00674 420662007773 dimer interface [polypeptide binding]; other site 420662007774 active site 420662007775 catalytic residue [active] 420662007776 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 420662007777 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 420662007778 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 420662007779 Cupin superfamily protein; Region: Cupin_4; pfam08007 420662007780 Cupin-like domain; Region: Cupin_8; pfam13621 420662007781 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 420662007782 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 420662007783 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 420662007784 trimer interface [polypeptide binding]; other site 420662007785 active site 420662007786 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 420662007787 Flavoprotein; Region: Flavoprotein; pfam02441 420662007788 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 420662007789 Predicted transcriptional regulators [Transcription]; Region: COG1510 420662007790 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 420662007791 dimerization interface [polypeptide binding]; other site 420662007792 putative DNA binding site [nucleotide binding]; other site 420662007793 putative Zn2+ binding site [ion binding]; other site 420662007794 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 420662007795 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 420662007796 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 420662007797 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662007798 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662007799 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 420662007800 dimerization interface [polypeptide binding]; other site 420662007801 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 420662007802 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 420662007803 NAD binding site [chemical binding]; other site 420662007804 catalytic residues [active] 420662007805 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 420662007806 thiS-thiF/thiG interaction site; other site 420662007807 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662007808 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662007809 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 420662007810 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 420662007811 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 420662007812 4Fe-4S dicluster domain; Region: Fer4_11; pfam13247 420662007813 PAS domain; Region: PAS; smart00091 420662007814 putative active site [active] 420662007815 heme pocket [chemical binding]; other site 420662007816 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 420662007817 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 420662007818 Walker A motif; other site 420662007819 ATP binding site [chemical binding]; other site 420662007820 Walker B motif; other site 420662007821 arginine finger; other site 420662007822 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662007823 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 420662007824 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 420662007825 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 420662007826 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 420662007827 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 420662007828 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 420662007829 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 420662007830 FeS/SAM binding site; other site 420662007831 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 420662007832 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 420662007833 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662007834 Walker A/P-loop; other site 420662007835 ATP binding site [chemical binding]; other site 420662007836 Q-loop/lid; other site 420662007837 ABC transporter signature motif; other site 420662007838 Walker B; other site 420662007839 D-loop; other site 420662007840 H-loop/switch region; other site 420662007841 ABC-2 type transporter; Region: ABC2_membrane; cl17235 420662007842 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 420662007843 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 420662007844 Transposase domain (DUF772); Region: DUF772; pfam05598 420662007845 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662007846 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662007847 Transposase domain (DUF772); Region: DUF772; pfam05598 420662007848 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 420662007849 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662007850 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662007851 Transposase domain (DUF772); Region: DUF772; pfam05598 420662007852 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662007853 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662007854 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662007855 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 420662007856 active site 420662007857 phosphorylation site [posttranslational modification] 420662007858 intermolecular recognition site; other site 420662007859 dimerization interface [polypeptide binding]; other site 420662007860 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 420662007861 DNA binding residues [nucleotide binding] 420662007862 dimerization interface [polypeptide binding]; other site 420662007863 Histidine kinase; Region: HisKA_3; pfam07730 420662007864 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 420662007865 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662007866 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 420662007867 N-terminal plug; other site 420662007868 ligand-binding site [chemical binding]; other site 420662007869 Predicted archaeal sugar kinases [General function prediction only]; Region: COG1907 420662007870 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 420662007871 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 420662007872 NAD(P) binding pocket [chemical binding]; other site 420662007873 Predicted ATP-dependent carboligase related to biotin carboxylase [General function prediction only]; Region: COG2232 420662007874 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662007875 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional; Region: PRK02264 420662007876 Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N...; Region: MCH; cd00545 420662007877 trimer interface I [polypeptide binding]; other site 420662007878 putative substrate binding pocket [chemical binding]; other site 420662007879 trimer interface II [polypeptide binding]; other site 420662007880 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 420662007881 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662007882 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; pfam01874 420662007883 formaldehyde-activating enzyme; Region: one_C_fae; TIGR03126 420662007884 Dihydroneopterin aldolase; Region: FolB; smart00905 420662007885 active site 420662007886 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662007887 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 420662007888 Walker A motif; other site 420662007889 ATP binding site [chemical binding]; other site 420662007890 Walker B motif; other site 420662007891 arginine finger; other site 420662007892 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662007893 archaeoflavoprotein AfpA; Region: archaeo_AfpA; TIGR02699 420662007894 Flavoprotein; Region: Flavoprotein; pfam02441 420662007895 dihydropteroate synthase-related protein; Region: TIGR00284 420662007896 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 420662007897 substrate binding pocket [chemical binding]; other site 420662007898 dimer interface [polypeptide binding]; other site 420662007899 inhibitor binding site; inhibition site 420662007900 Domain of unknown function (DUF4346); Region: DUF4346; pfam14251 420662007901 Protein of unknown function (DUF447); Region: DUF447; pfam04289 420662007902 hypothetical protein; Provisional; Region: PRK02227 420662007903 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 420662007904 nucleotide binding site [chemical binding]; other site 420662007905 substrate binding site [chemical binding]; other site 420662007906 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: COG1548; cl00668 420662007907 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662007908 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an...; Region: HisA_HisF; cd04723 420662007909 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 420662007910 active site 420662007911 The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea...; Region: MopB_FmdB-FwdB; cd02761 420662007912 formylmethanofuran dehydrogenase subunit B; Region: one_C_dehyd_B; TIGR03129 420662007913 putative [4Fe-4S] binding site [ion binding]; other site 420662007914 putative molybdopterin cofactor binding site [chemical binding]; other site 420662007915 formylmethanofuran dehydrogenase subunit A; Region: one_C_dehyd_A; TIGR03121 420662007916 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 420662007917 active site 420662007918 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional; Region: PRK02114 420662007919 Formylmethanofuran-tetrahydromethanopterin formyltransferase; Region: FTR; pfam01913 420662007920 FTR, proximal lobe; Region: FTR_C; pfam02741 420662007921 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 420662007922 domain_subunit interface; other site 420662007923 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 420662007924 aminodeoxychorismate synthase; Provisional; Region: PRK07508 420662007925 chorismate binding enzyme; Region: Chorismate_bind; cl10555 420662007926 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 420662007927 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 420662007928 substrate-cofactor binding pocket; other site 420662007929 homodimer interface [polypeptide binding]; other site 420662007930 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662007931 catalytic residue [active] 420662007932 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 420662007933 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 420662007934 putative GTP cyclohydrolase; Provisional; Region: PRK13674 420662007935 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 420662007936 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 420662007937 TPP-binding site; other site 420662007938 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 420662007939 PYR/PP interface [polypeptide binding]; other site 420662007940 dimer interface [polypeptide binding]; other site 420662007941 TPP binding site [chemical binding]; other site 420662007942 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 420662007943 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 420662007944 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 420662007945 substrate binding pocket [chemical binding]; other site 420662007946 chain length determination region; other site 420662007947 substrate-Mg2+ binding site; other site 420662007948 catalytic residues [active] 420662007949 aspartate-rich region 1; other site 420662007950 active site lid residues [active] 420662007951 aspartate-rich region 2; other site 420662007952 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 420662007953 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662007954 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 420662007955 [2Fe-2S] cluster binding site [ion binding]; other site 420662007956 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 420662007957 alpha subunit interface [polypeptide binding]; other site 420662007958 active site 420662007959 substrate binding site [chemical binding]; other site 420662007960 Fe binding site [ion binding]; other site 420662007961 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662007962 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 420662007963 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 420662007964 active site residue [active] 420662007965 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 420662007966 active site residue [active] 420662007967 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 420662007968 Ligand Binding Site [chemical binding]; other site 420662007969 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 420662007970 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 420662007971 active site 420662007972 substrate binding site [chemical binding]; other site 420662007973 cosubstrate binding site; other site 420662007974 catalytic site [active] 420662007975 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 420662007976 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 420662007977 active site 420662007978 HIGH motif; other site 420662007979 dimer interface [polypeptide binding]; other site 420662007980 KMSKS motif; other site 420662007981 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 420662007982 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 420662007983 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662007984 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 420662007985 dimer interface [polypeptide binding]; other site 420662007986 phosphorylation site [posttranslational modification] 420662007987 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 420662007988 ATP binding site [chemical binding]; other site 420662007989 G-X-G motif; other site 420662007990 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 420662007991 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 420662007992 active site 420662007993 phosphorylation site [posttranslational modification] 420662007994 intermolecular recognition site; other site 420662007995 dimerization interface [polypeptide binding]; other site 420662007996 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 420662007997 DNA binding site [nucleotide binding] 420662007998 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 420662007999 dimer interface [polypeptide binding]; other site 420662008000 Pirin-related protein [General function prediction only]; Region: COG1741 420662008001 Pirin; Region: Pirin; pfam02678 420662008002 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 420662008003 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 420662008004 active site 1 [active] 420662008005 dimer interface [polypeptide binding]; other site 420662008006 hexamer interface [polypeptide binding]; other site 420662008007 active site 2 [active] 420662008008 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 420662008009 Esterase PHB depolymerase; Region: Esterase_phd; pfam10503 420662008010 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 420662008011 Helix-turn-helix domain; Region: HTH_18; pfam12833 420662008012 Cytochrome c; Region: Cytochrom_C; pfam00034 420662008013 Methylamine dehydrogenase, L chain; Region: Me-amine-dh_L; cl03812 420662008014 Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for...; Region: mauD; cd02967 420662008015 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662008016 catalytic residues [active] 420662008017 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_1; cd09996 420662008018 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 420662008019 active site 420662008020 Zn binding site [ion binding]; other site 420662008021 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 420662008022 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 420662008023 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662008024 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 420662008025 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 420662008026 substrate binding site [chemical binding]; other site 420662008027 oxyanion hole (OAH) forming residues; other site 420662008028 trimer interface [polypeptide binding]; other site 420662008029 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 420662008030 Methyltransferase domain; Region: Methyltransf_23; pfam13489 420662008031 Methyltransferase domain; Region: Methyltransf_11; pfam08241 420662008032 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 420662008033 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 420662008034 dimerization interface [polypeptide binding]; other site 420662008035 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662008036 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662008037 dimer interface [polypeptide binding]; other site 420662008038 putative CheW interface [polypeptide binding]; other site 420662008039 HAMP domain; Region: HAMP; pfam00672 420662008040 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 420662008041 PAS domain; Region: PAS_9; pfam13426 420662008042 putative active site [active] 420662008043 heme pocket [chemical binding]; other site 420662008044 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662008045 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662008046 metal binding site [ion binding]; metal-binding site 420662008047 active site 420662008048 I-site; other site 420662008049 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 420662008050 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 420662008051 TPR motif; other site 420662008052 binding surface 420662008053 short chain dehydrogenase; Provisional; Region: PRK09072 420662008054 classical (c) SDRs; Region: SDR_c; cd05233 420662008055 active site 420662008056 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 420662008057 heme binding pocket [chemical binding]; other site 420662008058 heme ligand [chemical binding]; other site 420662008059 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_3; cd05914 420662008060 acyl-activating enzyme (AAE) consensus motif; other site 420662008061 putative AMP binding site [chemical binding]; other site 420662008062 putative active site [active] 420662008063 putative CoA binding site [chemical binding]; other site 420662008064 Thermostable hemolysin; Region: T_hemolysin; pfam12261 420662008065 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 420662008066 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662008067 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 420662008068 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 420662008069 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 420662008070 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 420662008071 active site 420662008072 DNA-binding transcriptional activator MhpR; Provisional; Region: PRK09834 420662008073 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 420662008074 Bacterial transcriptional regulator; Region: IclR; pfam01614 420662008075 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662008076 trimer interface [polypeptide binding]; other site 420662008077 eyelet of channel; other site 420662008078 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662008079 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 420662008080 Sulfatase; Region: Sulfatase; pfam00884 420662008081 Uncharacterized conserved protein [Function unknown]; Region: COG1262 420662008082 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 420662008083 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 420662008084 DNA binding residues [nucleotide binding] 420662008085 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 420662008086 putative dimer interface [polypeptide binding]; other site 420662008087 putative metal binding residues [ion binding]; other site 420662008088 Protein of unknown function (DUF2938); Region: DUF2938; pfam11158 420662008089 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 420662008090 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662008091 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 420662008092 PAS domain; Region: PAS_9; pfam13426 420662008093 putative active site [active] 420662008094 heme pocket [chemical binding]; other site 420662008095 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 420662008096 DNA binding residues [nucleotide binding] 420662008097 dimerization interface [polypeptide binding]; other site 420662008098 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 420662008099 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662008100 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 420662008101 acyl-activating enzyme (AAE) consensus motif; other site 420662008102 acyl-activating enzyme (AAE) consensus motif; other site 420662008103 putative AMP binding site [chemical binding]; other site 420662008104 putative active site [active] 420662008105 putative CoA binding site [chemical binding]; other site 420662008106 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662008107 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662008108 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662008109 C-terminal domain of Burkholderia sp. NF100 MhqB and similar proteins; MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion; Region: MhqB_like_C; cd08360 420662008110 putative active site [active] 420662008111 Isochorismatase family; Region: Isochorismatase; pfam00857 420662008112 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 420662008113 catalytic triad [active] 420662008114 dimer interface [polypeptide binding]; other site 420662008115 conserved cis-peptide bond; other site 420662008116 seryl-tRNA synthetase; Provisional; Region: PRK05431 420662008117 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 420662008118 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 420662008119 dimer interface [polypeptide binding]; other site 420662008120 active site 420662008121 motif 1; other site 420662008122 motif 2; other site 420662008123 motif 3; other site 420662008124 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 420662008125 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 420662008126 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 420662008127 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 420662008128 hypothetical protein; Reviewed; Region: PRK00024 420662008129 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 420662008130 MPN+ (JAMM) motif; other site 420662008131 Zinc-binding site [ion binding]; other site 420662008132 Smr domain; Region: Smr; pfam01713 420662008133 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 420662008134 apolar tunnel; other site 420662008135 heme binding site [chemical binding]; other site 420662008136 dimerization interface [polypeptide binding]; other site 420662008137 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 420662008138 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 420662008139 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 420662008140 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662008141 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662008142 metal binding site [ion binding]; metal-binding site 420662008143 active site 420662008144 I-site; other site 420662008145 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 420662008146 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 420662008147 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 420662008148 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 420662008149 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 420662008150 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 420662008151 active site 420662008152 phosphorylation site [posttranslational modification] 420662008153 intermolecular recognition site; other site 420662008154 dimerization interface [polypeptide binding]; other site 420662008155 CheB methylesterase; Region: CheB_methylest; pfam01339 420662008156 HemN family oxidoreductase; Provisional; Region: PRK05660 420662008157 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 420662008158 FeS/SAM binding site; other site 420662008159 HemN C-terminal domain; Region: HemN_C; pfam06969 420662008160 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 420662008161 active site 420662008162 dimerization interface [polypeptide binding]; other site 420662008163 ribonuclease PH; Reviewed; Region: rph; PRK00173 420662008164 Ribonuclease PH; Region: RNase_PH_bact; cd11362 420662008165 hexamer interface [polypeptide binding]; other site 420662008166 active site 420662008167 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 420662008168 Protein phosphatase 2C; Region: PP2C; pfam00481 420662008169 active site 420662008170 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662008171 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662008172 active site 420662008173 ATP binding site [chemical binding]; other site 420662008174 substrate binding site [chemical binding]; other site 420662008175 activation loop (A-loop); other site 420662008176 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662008177 hypothetical protein; Provisional; Region: PRK11820 420662008178 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 420662008179 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 420662008180 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 420662008181 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 420662008182 active site 420662008183 Int/Topo IB signature motif; other site 420662008184 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 420662008185 transcriptional regulator, y4mF family; Region: couple_hipB; TIGR03070 420662008186 non-specific DNA binding site [nucleotide binding]; other site 420662008187 salt bridge; other site 420662008188 sequence-specific DNA binding site [nucleotide binding]; other site 420662008189 HipA N-terminal domain; Region: Couple_hipA; pfam13657 420662008190 HipA-like N-terminal domain; Region: HipA_N; pfam07805 420662008191 HipA-like C-terminal domain; Region: HipA_C; pfam07804 420662008192 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 420662008193 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 420662008194 catalytic site [active] 420662008195 G-X2-G-X-G-K; other site 420662008196 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 420662008197 Predicted transporter component [General function prediction only]; Region: COG2391 420662008198 Sulphur transport; Region: Sulf_transp; pfam04143 420662008199 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 420662008200 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 420662008201 putative DNA binding site [nucleotide binding]; other site 420662008202 dimerization interface [polypeptide binding]; other site 420662008203 putative Zn2+ binding site [ion binding]; other site 420662008204 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662008205 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 420662008206 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662008207 Zn2+ binding site [ion binding]; other site 420662008208 Mg2+ binding site [ion binding]; other site 420662008209 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 420662008210 synthetase active site [active] 420662008211 NTP binding site [chemical binding]; other site 420662008212 metal binding site [ion binding]; metal-binding site 420662008213 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 420662008214 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 420662008215 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 420662008216 CoA-transferase family III; Region: CoA_transf_3; pfam02515 420662008217 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 420662008218 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 420662008219 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 420662008220 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 420662008221 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 420662008222 active site 420662008223 dimer interface [polypeptide binding]; other site 420662008224 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 420662008225 Ligand Binding Site [chemical binding]; other site 420662008226 Molecular Tunnel; other site 420662008227 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 420662008228 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 420662008229 active site 420662008230 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 420662008231 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662008232 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 420662008233 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 420662008234 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 420662008235 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 420662008236 Substrate binding site; other site 420662008237 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 420662008238 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 420662008239 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 420662008240 NADP binding site [chemical binding]; other site 420662008241 active site 420662008242 putative substrate binding site [chemical binding]; other site 420662008243 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 420662008244 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 420662008245 NADP-binding site; other site 420662008246 homotetramer interface [polypeptide binding]; other site 420662008247 substrate binding site [chemical binding]; other site 420662008248 homodimer interface [polypeptide binding]; other site 420662008249 active site 420662008250 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 420662008251 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 420662008252 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 420662008253 chain length determinant protein EpsF; Region: EpsF; TIGR03017 420662008254 Chain length determinant protein; Region: Wzz; pfam02706 420662008255 Chain length determinant protein; Region: Wzz; cl15801 420662008256 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 420662008257 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 420662008258 SLBB domain; Region: SLBB; pfam10531 420662008259 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 420662008260 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 420662008261 S-adenosylmethionine binding site [chemical binding]; other site 420662008262 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 420662008263 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 420662008264 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 420662008265 HIT family signature motif; other site 420662008266 catalytic residue [active] 420662008267 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 420662008268 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 420662008269 FAD binding domain; Region: FAD_binding_4; pfam01565 420662008270 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 420662008271 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 420662008272 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 420662008273 Cysteine-rich domain; Region: CCG; pfam02754 420662008274 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 420662008275 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 420662008276 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 420662008277 active site 420662008278 catalytic site [active] 420662008279 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 420662008280 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662008281 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662008282 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 420662008283 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662008284 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 420662008285 dimer interface [polypeptide binding]; other site 420662008286 phosphorylation site [posttranslational modification] 420662008287 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 420662008288 ATP binding site [chemical binding]; other site 420662008289 Mg2+ binding site [ion binding]; other site 420662008290 G-X-G motif; other site 420662008291 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 420662008292 heterotetramer interface [polypeptide binding]; other site 420662008293 active site pocket [active] 420662008294 cleavage site 420662008295 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 420662008296 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 420662008297 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 420662008298 SEC-C motif; Region: SEC-C; pfam02810 420662008299 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 420662008300 Peptidase family M23; Region: Peptidase_M23; pfam01551 420662008301 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 420662008302 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 420662008303 Walker A/P-loop; other site 420662008304 ATP binding site [chemical binding]; other site 420662008305 Q-loop/lid; other site 420662008306 ABC transporter signature motif; other site 420662008307 Walker B; other site 420662008308 D-loop; other site 420662008309 H-loop/switch region; other site 420662008310 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 420662008311 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 420662008312 FtsX-like permease family; Region: FtsX; pfam02687 420662008313 TraB family; Region: TraB; pfam01963 420662008314 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 420662008315 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 420662008316 DHH family; Region: DHH; pfam01368 420662008317 DHHA1 domain; Region: DHHA1; pfam02272 420662008318 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 420662008319 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 420662008320 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 420662008321 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 420662008322 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 420662008323 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 420662008324 active site 420662008325 phosphorylation site [posttranslational modification] 420662008326 intermolecular recognition site; other site 420662008327 dimerization interface [polypeptide binding]; other site 420662008328 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 420662008329 DNA binding site [nucleotide binding] 420662008330 sensor protein QseC; Provisional; Region: PRK10337 420662008331 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 420662008332 dimer interface [polypeptide binding]; other site 420662008333 phosphorylation site [posttranslational modification] 420662008334 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 420662008335 ATP binding site [chemical binding]; other site 420662008336 Mg2+ binding site [ion binding]; other site 420662008337 G-X-G motif; other site 420662008338 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 420662008339 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 420662008340 active site 420662008341 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 420662008342 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 420662008343 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 420662008344 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 420662008345 homotrimer interaction site [polypeptide binding]; other site 420662008346 putative active site [active] 420662008347 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 420662008348 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 420662008349 putative deacylase active site [active] 420662008350 Biofilm formation and stress response factor; Region: BsmA; pfam10014 420662008351 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 420662008352 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662008353 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662008354 Walker A/P-loop; other site 420662008355 ATP binding site [chemical binding]; other site 420662008356 Q-loop/lid; other site 420662008357 ABC transporter signature motif; other site 420662008358 Walker B; other site 420662008359 D-loop; other site 420662008360 H-loop/switch region; other site 420662008361 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 420662008362 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 420662008363 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 420662008364 putative active site [active] 420662008365 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662008366 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 420662008367 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 420662008368 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 420662008369 inhibitor-cofactor binding pocket; inhibition site 420662008370 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662008371 catalytic residue [active] 420662008372 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 420662008373 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 420662008374 putative trimer interface [polypeptide binding]; other site 420662008375 putative CoA binding site [chemical binding]; other site 420662008376 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662008377 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 420662008378 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 420662008379 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662008380 metal-binding site 420662008381 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 420662008382 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 420662008383 putative metal binding site; other site 420662008384 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662008385 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 420662008386 peptide chain release factor 2; Validated; Region: prfB; PRK00578 420662008387 This domain is found in peptide chain release factors; Region: PCRF; smart00937 420662008388 RF-1 domain; Region: RF-1; pfam00472 420662008389 aminopeptidase N; Provisional; Region: pepN; PRK14015 420662008390 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 420662008391 Zn binding site [ion binding]; other site 420662008392 fructose-1,6-bisphosphatase family protein; Region: PLN02628 420662008393 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 420662008394 AMP binding site [chemical binding]; other site 420662008395 metal binding site [ion binding]; metal-binding site 420662008396 active site 420662008397 6-phosphofructokinase; Provisional; Region: PRK14072 420662008398 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 420662008399 active site 420662008400 ADP/pyrophosphate binding site [chemical binding]; other site 420662008401 dimerization interface [polypeptide binding]; other site 420662008402 allosteric effector site; other site 420662008403 fructose-1,6-bisphosphate binding site; other site 420662008404 TspO/MBR family; Region: TspO_MBR; pfam03073 420662008405 geranylgeranyl reductase; Region: BchP-ChlP; TIGR02023 420662008406 PAS domain; Region: PAS_9; pfam13426 420662008407 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 420662008408 putative active site [active] 420662008409 heme pocket [chemical binding]; other site 420662008410 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662008411 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662008412 dimer interface [polypeptide binding]; other site 420662008413 putative CheW interface [polypeptide binding]; other site 420662008414 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662008415 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662008416 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 420662008417 putative dimerization interface [polypeptide binding]; other site 420662008418 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 420662008419 Ribulose bisphosphate carboxylase large chain, Form I; Region: RuBisCO_large_I; cd08212 420662008420 homodimer interface [polypeptide binding]; other site 420662008421 active site 420662008422 heterodimer interface [polypeptide binding]; other site 420662008423 catalytic residue [active] 420662008424 metal binding site [ion binding]; metal-binding site 420662008425 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 420662008426 multimerization interface [polypeptide binding]; other site 420662008427 probable Rubsico expression protein CbbX; Region: cbbX_cfxQ; TIGR02880 420662008428 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 420662008429 Walker A motif; other site 420662008430 ATP binding site [chemical binding]; other site 420662008431 Walker B motif; other site 420662008432 arginine finger; other site 420662008433 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 420662008434 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 420662008435 motif II; other site 420662008436 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 420662008437 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 420662008438 substrate binding site [chemical binding]; other site 420662008439 hexamer interface [polypeptide binding]; other site 420662008440 metal binding site [ion binding]; metal-binding site 420662008441 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 420662008442 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 420662008443 motif II; other site 420662008444 fructose-1,6-bisphosphatase family protein; Region: PLN02628 420662008445 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 420662008446 AMP binding site [chemical binding]; other site 420662008447 metal binding site [ion binding]; metal-binding site 420662008448 active site 420662008449 phosphoribulokinase; Provisional; Region: PRK15453 420662008450 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 420662008451 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 420662008452 TPP-binding site [chemical binding]; other site 420662008453 dimer interface [polypeptide binding]; other site 420662008454 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 420662008455 PYR/PP interface [polypeptide binding]; other site 420662008456 dimer interface [polypeptide binding]; other site 420662008457 TPP binding site [chemical binding]; other site 420662008458 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 420662008459 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 420662008460 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 420662008461 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 420662008462 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 420662008463 Phosphoglycerate kinase; Region: PGK; pfam00162 420662008464 substrate binding site [chemical binding]; other site 420662008465 hinge regions; other site 420662008466 ADP binding site [chemical binding]; other site 420662008467 catalytic site [active] 420662008468 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 420662008469 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 420662008470 intersubunit interface [polypeptide binding]; other site 420662008471 active site 420662008472 zinc binding site [ion binding]; other site 420662008473 Na+ binding site [ion binding]; other site 420662008474 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 420662008475 CreA protein; Region: CreA; pfam05981 420662008476 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 420662008477 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 420662008478 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 420662008479 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 420662008480 putative active site [active] 420662008481 heme pocket [chemical binding]; other site 420662008482 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 420662008483 dimer interface [polypeptide binding]; other site 420662008484 phosphorylation site [posttranslational modification] 420662008485 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 420662008486 ATP binding site [chemical binding]; other site 420662008487 G-X-G motif; other site 420662008488 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662008489 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 420662008490 N-terminal plug; other site 420662008491 ligand-binding site [chemical binding]; other site 420662008492 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 420662008493 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 420662008494 Walker A/P-loop; other site 420662008495 ATP binding site [chemical binding]; other site 420662008496 Q-loop/lid; other site 420662008497 ABC transporter signature motif; other site 420662008498 Walker B; other site 420662008499 D-loop; other site 420662008500 H-loop/switch region; other site 420662008501 ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]; Region: CbiM; cl00397 420662008502 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 420662008503 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 420662008504 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662008505 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 420662008506 N-terminal plug; other site 420662008507 ligand-binding site [chemical binding]; other site 420662008508 nickel responsive regulator; Provisional; Region: PRK02967 420662008509 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 420662008510 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 420662008511 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 420662008512 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 420662008513 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 420662008514 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 420662008515 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 420662008516 active site 420662008517 phosphorylation site [posttranslational modification] 420662008518 intermolecular recognition site; other site 420662008519 dimerization interface [polypeptide binding]; other site 420662008520 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 420662008521 Walker A motif; other site 420662008522 ATP binding site [chemical binding]; other site 420662008523 Walker B motif; other site 420662008524 arginine finger; other site 420662008525 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662008526 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 420662008527 putative active site [active] 420662008528 putative substrate binding site [chemical binding]; other site 420662008529 putative cosubstrate binding site; other site 420662008530 catalytic site [active] 420662008531 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 420662008532 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 420662008533 substrate binding site [chemical binding]; other site 420662008534 oxyanion hole (OAH) forming residues; other site 420662008535 trimer interface [polypeptide binding]; other site 420662008536 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 420662008537 dimerization interface [polypeptide binding]; other site 420662008538 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 420662008539 ATP binding site [chemical binding]; other site 420662008540 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 420662008541 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 420662008542 HupF/HypC family; Region: HupF_HypC; pfam01455 420662008543 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 420662008544 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 420662008545 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 420662008546 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 420662008547 zinc-finger; Region: zf-RING_3; pfam14369 420662008548 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 420662008549 Protein of unknown function (DUF3457); Region: DUF3457; pfam11939 420662008550 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 420662008551 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 420662008552 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 420662008553 HupF/HypC family; Region: HupF_HypC; pfam01455 420662008554 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 420662008555 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 420662008556 putative substrate-binding site; other site 420662008557 nickel binding site [ion binding]; other site 420662008558 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 420662008559 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 420662008560 non-specific DNA binding site [nucleotide binding]; other site 420662008561 salt bridge; other site 420662008562 sequence-specific DNA binding site [nucleotide binding]; other site 420662008563 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 420662008564 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 420662008565 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 420662008566 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 420662008567 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 420662008568 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 420662008569 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 420662008570 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 420662008571 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 420662008572 phosphate binding site [ion binding]; other site 420662008573 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 420662008574 hypothetical protein; Provisional; Region: PRK05409 420662008575 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 420662008576 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 420662008577 DctM-like transporters; Region: DctM; pfam06808 420662008578 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 420662008579 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 420662008580 peptidase PmbA; Provisional; Region: PRK11040 420662008581 Protein of unknown function (DUF615); Region: DUF615; pfam04751 420662008582 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 420662008583 MPT binding site; other site 420662008584 trimer interface [polypeptide binding]; other site 420662008585 serine O-acetyltransferase; Region: cysE; TIGR01172 420662008586 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 420662008587 trimer interface [polypeptide binding]; other site 420662008588 active site 420662008589 substrate binding site [chemical binding]; other site 420662008590 CoA binding site [chemical binding]; other site 420662008591 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 420662008592 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 420662008593 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 420662008594 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 420662008595 active site 420662008596 dimerization interface [polypeptide binding]; other site 420662008597 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 420662008598 MutS domain I; Region: MutS_I; pfam01624 420662008599 MutS domain II; Region: MutS_II; pfam05188 420662008600 MutS domain III; Region: MutS_III; pfam05192 420662008601 MutS domain V; Region: MutS_V; pfam00488 420662008602 Walker A/P-loop; other site 420662008603 ATP binding site [chemical binding]; other site 420662008604 Q-loop/lid; other site 420662008605 ABC transporter signature motif; other site 420662008606 Walker B; other site 420662008607 D-loop; other site 420662008608 H-loop/switch region; other site 420662008609 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 420662008610 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 420662008611 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662008612 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 420662008613 CTP synthetase; Validated; Region: pyrG; PRK05380 420662008614 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 420662008615 Catalytic site [active] 420662008616 active site 420662008617 UTP binding site [chemical binding]; other site 420662008618 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 420662008619 active site 420662008620 putative oxyanion hole; other site 420662008621 catalytic triad [active] 420662008622 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 420662008623 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 420662008624 enolase; Provisional; Region: eno; PRK00077 420662008625 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 420662008626 dimer interface [polypeptide binding]; other site 420662008627 metal binding site [ion binding]; metal-binding site 420662008628 substrate binding pocket [chemical binding]; other site 420662008629 Septum formation initiator; Region: DivIC; cl17659 420662008630 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 420662008631 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 420662008632 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 420662008633 S-adenosylmethionine binding site [chemical binding]; other site 420662008634 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 420662008635 classical (c) SDRs; Region: SDR_c; cd05233 420662008636 NAD(P) binding site [chemical binding]; other site 420662008637 active site 420662008638 Domain of unknown function DUF21; Region: DUF21; pfam01595 420662008639 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 420662008640 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 420662008641 Transporter associated domain; Region: CorC_HlyC; smart01091 420662008642 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 420662008643 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 420662008644 active site 420662008645 metal binding site [ion binding]; metal-binding site 420662008646 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662008647 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662008648 metal binding site [ion binding]; metal-binding site 420662008649 active site 420662008650 I-site; other site 420662008651 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 420662008652 Response regulator receiver domain; Region: Response_reg; pfam00072 420662008653 active site 420662008654 phosphorylation site [posttranslational modification] 420662008655 intermolecular recognition site; other site 420662008656 PAS fold; Region: PAS; pfam00989 420662008657 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 420662008658 putative active site [active] 420662008659 heme pocket [chemical binding]; other site 420662008660 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662008661 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662008662 metal binding site [ion binding]; metal-binding site 420662008663 active site 420662008664 I-site; other site 420662008665 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 420662008666 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 420662008667 dimerization interface [polypeptide binding]; other site 420662008668 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 420662008669 dimer interface [polypeptide binding]; other site 420662008670 phosphorylation site [posttranslational modification] 420662008671 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 420662008672 ATP binding site [chemical binding]; other site 420662008673 Mg2+ binding site [ion binding]; other site 420662008674 G-X-G motif; other site 420662008675 Response regulator receiver domain; Region: Response_reg; pfam00072 420662008676 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 420662008677 active site 420662008678 phosphorylation site [posttranslational modification] 420662008679 intermolecular recognition site; other site 420662008680 dimerization interface [polypeptide binding]; other site 420662008681 Response regulator receiver domain; Region: Response_reg; pfam00072 420662008682 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 420662008683 active site 420662008684 phosphorylation site [posttranslational modification] 420662008685 intermolecular recognition site; other site 420662008686 dimerization interface [polypeptide binding]; other site 420662008687 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 420662008688 putative binding surface; other site 420662008689 active site 420662008690 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 420662008691 ATP binding site [chemical binding]; other site 420662008692 Mg2+ binding site [ion binding]; other site 420662008693 G-X-G motif; other site 420662008694 Response regulator receiver domain; Region: Response_reg; pfam00072 420662008695 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 420662008696 active site 420662008697 phosphorylation site [posttranslational modification] 420662008698 intermolecular recognition site; other site 420662008699 dimerization interface [polypeptide binding]; other site 420662008700 PAS domain; Region: PAS; smart00091 420662008701 PAS fold; Region: PAS; pfam00989 420662008702 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 420662008703 putative active site [active] 420662008704 heme pocket [chemical binding]; other site 420662008705 PAS domain; Region: PAS_9; pfam13426 420662008706 PAS domain; Region: PAS_8; pfam13188 420662008707 PAS domain; Region: PAS_9; pfam13426 420662008708 PAS fold; Region: PAS_4; pfam08448 420662008709 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 420662008710 Histidine kinase; Region: HisKA_2; pfam07568 420662008711 Flagellar regulator YcgR; Region: YcgR; pfam07317 420662008712 PilZ domain; Region: PilZ; pfam07238 420662008713 Flagellar protein FliT; Region: FliT; pfam05400 420662008714 Flagellar protein FliS; Region: FliS; cl00654 420662008715 flagellar capping protein; Reviewed; Region: fliD; PRK08032 420662008716 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 420662008717 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 420662008718 flagellin; Reviewed; Region: PRK08869 420662008719 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 420662008720 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 420662008721 flagellin; Reviewed; Region: PRK08869 420662008722 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 420662008723 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 420662008724 Flagellar transcriptional activator (FlhD); Region: FlhD; pfam05247 420662008725 transcriptional activator FlhC; Provisional; Region: PRK12722 420662008726 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 420662008727 flagellar motor protein MotA; Validated; Region: PRK09110 420662008728 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 420662008729 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662008730 ligand binding site [chemical binding]; other site 420662008731 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 420662008732 rhodanese superfamily protein; Provisional; Region: PRK05320 420662008733 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; cl00125 420662008734 active site residue [active] 420662008735 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 420662008736 proposed catalytic triad [active] 420662008737 active site nucleophile [active] 420662008738 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 420662008739 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 420662008740 substrate binding pocket [chemical binding]; other site 420662008741 membrane-bound complex binding site; other site 420662008742 hinge residues; other site 420662008743 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 420662008744 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 420662008745 dimer interface [polypeptide binding]; other site 420662008746 conserved gate region; other site 420662008747 putative PBP binding loops; other site 420662008748 ABC-ATPase subunit interface; other site 420662008749 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 420662008750 dimer interface [polypeptide binding]; other site 420662008751 conserved gate region; other site 420662008752 putative PBP binding loops; other site 420662008753 ABC-ATPase subunit interface; other site 420662008754 Predicted deacylase [General function prediction only]; Region: COG3608 420662008755 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 420662008756 active site 420662008757 Zn binding site [ion binding]; other site 420662008758 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 420662008759 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 420662008760 Walker A/P-loop; other site 420662008761 ATP binding site [chemical binding]; other site 420662008762 Q-loop/lid; other site 420662008763 ABC transporter signature motif; other site 420662008764 Walker B; other site 420662008765 D-loop; other site 420662008766 H-loop/switch region; other site 420662008767 Protein of unknown function, DUF599; Region: DUF599; pfam04654 420662008768 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662008769 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662008770 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 420662008771 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 420662008772 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662008773 Predicted flavoprotein [General function prediction only]; Region: COG0431 420662008774 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 420662008775 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662008776 Pirin-related protein [General function prediction only]; Region: COG1741 420662008777 Pirin; Region: Pirin; pfam02678 420662008778 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 420662008779 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662008780 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 420662008781 dimerization interface [polypeptide binding]; other site 420662008782 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 420662008783 Malonate decarboxylase gamma subunit (MdcE); Region: MdcE; pfam06833 420662008784 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 420662008785 malonate decarboxylase acyl carrier protein; Region: malonate_delta; TIGR03130 420662008786 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 420662008787 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 420662008788 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662008789 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662008790 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 420662008791 dimerization interface [polypeptide binding]; other site 420662008792 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662008793 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662008794 DNA-binding site [nucleotide binding]; DNA binding site 420662008795 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 420662008796 FCD domain; Region: FCD; pfam07729 420662008797 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 420662008798 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 420662008799 active site 420662008800 HIGH motif; other site 420662008801 nucleotide binding site [chemical binding]; other site 420662008802 active site 420662008803 KMSKS motif; other site 420662008804 Response regulator receiver domain; Region: Response_reg; pfam00072 420662008805 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 420662008806 active site 420662008807 phosphorylation site [posttranslational modification] 420662008808 intermolecular recognition site; other site 420662008809 dimerization interface [polypeptide binding]; other site 420662008810 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662008811 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 420662008812 active site 420662008813 phosphorylation site [posttranslational modification] 420662008814 intermolecular recognition site; other site 420662008815 dimerization interface [polypeptide binding]; other site 420662008816 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 420662008817 DNA binding residues [nucleotide binding] 420662008818 dimerization interface [polypeptide binding]; other site 420662008819 CHASE3 domain; Region: CHASE3; pfam05227 420662008820 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 420662008821 Histidine kinase; Region: HisKA_3; pfam07730 420662008822 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 420662008823 ATP binding site [chemical binding]; other site 420662008824 Mg2+ binding site [ion binding]; other site 420662008825 G-X-G motif; other site 420662008826 BON domain; Region: BON; pfam04972 420662008827 hypothetical protein; Provisional; Region: PRK10428 420662008828 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 420662008829 catalytic site [active] 420662008830 putative active site [active] 420662008831 putative substrate binding site [chemical binding]; other site 420662008832 dimer interface [polypeptide binding]; other site 420662008833 Peptidase family M48; Region: Peptidase_M48; pfam01435 420662008834 GTPase RsgA; Reviewed; Region: PRK00098 420662008835 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 420662008836 RNA binding site [nucleotide binding]; other site 420662008837 homodimer interface [polypeptide binding]; other site 420662008838 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 420662008839 GTPase/Zn-binding domain interface [polypeptide binding]; other site 420662008840 GTP/Mg2+ binding site [chemical binding]; other site 420662008841 G4 box; other site 420662008842 G5 box; other site 420662008843 G1 box; other site 420662008844 Switch I region; other site 420662008845 G2 box; other site 420662008846 G3 box; other site 420662008847 Switch II region; other site 420662008848 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662008849 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662008850 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 420662008851 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 420662008852 DNA binding residues [nucleotide binding] 420662008853 dimerization interface [polypeptide binding]; other site 420662008854 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 420662008855 helicase 45; Provisional; Region: PTZ00424 420662008856 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 420662008857 ATP binding site [chemical binding]; other site 420662008858 Mg++ binding site [ion binding]; other site 420662008859 motif III; other site 420662008860 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 420662008861 nucleotide binding region [chemical binding]; other site 420662008862 ATP-binding site [chemical binding]; other site 420662008863 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 420662008864 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 420662008865 PAS domain; Region: PAS_9; pfam13426 420662008866 putative active site [active] 420662008867 heme pocket [chemical binding]; other site 420662008868 HAMP domain; Region: HAMP; pfam00672 420662008869 dimerization interface [polypeptide binding]; other site 420662008870 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662008871 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662008872 dimer interface [polypeptide binding]; other site 420662008873 putative CheW interface [polypeptide binding]; other site 420662008874 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 420662008875 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662008876 NAD(P) binding site [chemical binding]; other site 420662008877 active site 420662008878 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 420662008879 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 420662008880 putative substrate translocation pore; other site 420662008881 Transcriptional regulators [Transcription]; Region: MarR; COG1846 420662008882 MarR family; Region: MarR_2; pfam12802 420662008883 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 420662008884 CoenzymeA binding site [chemical binding]; other site 420662008885 subunit interaction site [polypeptide binding]; other site 420662008886 PHB binding site; other site 420662008887 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662008888 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 420662008889 dimer interface [polypeptide binding]; other site 420662008890 active site 420662008891 metal binding site [ion binding]; metal-binding site 420662008892 glutathione binding site [chemical binding]; other site 420662008893 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 420662008894 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 420662008895 putative active site pocket [active] 420662008896 dimerization interface [polypeptide binding]; other site 420662008897 putative catalytic residue [active] 420662008898 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 420662008899 Domain of unknown function DUF20; Region: UPF0118; pfam01594 420662008900 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 420662008901 Ligand binding site; other site 420662008902 metal-binding site 420662008903 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 420662008904 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 420662008905 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 420662008906 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 420662008907 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 420662008908 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 420662008909 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 420662008910 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 420662008911 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 420662008912 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 420662008913 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662008914 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 420662008915 N-terminal plug; other site 420662008916 ligand-binding site [chemical binding]; other site 420662008917 methionine sulfoxide reductase A; Provisional; Region: PRK14054 420662008918 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 420662008919 putative active site [active] 420662008920 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 420662008921 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 420662008922 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 420662008923 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662008924 catalytic residue [active] 420662008925 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 420662008926 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 420662008927 dimer interface [polypeptide binding]; other site 420662008928 active site 420662008929 glycine-pyridoxal phosphate binding site [chemical binding]; other site 420662008930 folate binding site [chemical binding]; other site 420662008931 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 420662008932 ATP cone domain; Region: ATP-cone; pfam03477 420662008933 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 420662008934 Type II transport protein GspH; Region: GspH; pfam12019 420662008935 hypothetical protein; Provisional; Region: PRK10557 420662008936 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 420662008937 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 420662008938 catalytic motif [active] 420662008939 Zn binding site [ion binding]; other site 420662008940 RibD C-terminal domain; Region: RibD_C; cl17279 420662008941 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 420662008942 Lumazine binding domain; Region: Lum_binding; pfam00677 420662008943 Lumazine binding domain; Region: Lum_binding; pfam00677 420662008944 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 420662008945 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 420662008946 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 420662008947 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 420662008948 homopentamer interface [polypeptide binding]; other site 420662008949 active site 420662008950 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 420662008951 putative RNA binding site [nucleotide binding]; other site 420662008952 aminotransferase; Validated; Region: PRK07337 420662008953 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 420662008954 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662008955 homodimer interface [polypeptide binding]; other site 420662008956 catalytic residue [active] 420662008957 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662008958 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662008959 active site 420662008960 ATP binding site [chemical binding]; other site 420662008961 substrate binding site [chemical binding]; other site 420662008962 activation loop (A-loop); other site 420662008963 PEGA domain; Region: PEGA; pfam08308 420662008964 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 420662008965 active site 420662008966 TolQ protein; Region: tolQ; TIGR02796 420662008967 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662008968 TolR protein; Region: tolR; TIGR02801 420662008969 TolA protein; Region: tolA_full; TIGR02794 420662008970 TonB C terminal; Region: TonB_2; pfam13103 420662008971 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 420662008972 hypothetical protein; Provisional; Region: PRK05409 420662008973 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 420662008974 RNA polymerase sigma factor; Provisional; Region: PRK12520 420662008975 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662008976 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 420662008977 DNA binding residues [nucleotide binding] 420662008978 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662008979 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 420662008980 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 420662008981 Transposase domain (DUF772); Region: DUF772; pfam05598 420662008982 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662008983 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662008984 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 420662008985 Protein export membrane protein; Region: SecD_SecF; cl14618 420662008986 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662008987 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662008988 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662008989 5-oxoprolinase; Region: PLN02666 420662008990 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 420662008991 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 420662008992 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 420662008993 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 420662008994 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 420662008995 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 420662008996 Walker A motif; other site 420662008997 ATP binding site [chemical binding]; other site 420662008998 Walker B motif; other site 420662008999 CheW-like domain; Region: CheW; pfam01584 420662009000 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 420662009001 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662009002 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 420662009003 active site 420662009004 substrate binding site [chemical binding]; other site 420662009005 activation loop (A-loop); other site 420662009006 HDOD domain; Region: HDOD; pfam08668 420662009007 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 420662009008 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 420662009009 Cupin domain; Region: Cupin_2; pfam07883 420662009010 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 420662009011 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662009012 Predicted transcriptional regulator [Transcription]; Region: COG1959 420662009013 Transcriptional regulator; Region: Rrf2; pfam02082 420662009014 HNH endonuclease; Region: HNH_2; pfam13391 420662009015 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 420662009016 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 420662009017 catalytic residues [active] 420662009018 catalytic nucleophile [active] 420662009019 Recombinase; Region: Recombinase; pfam07508 420662009020 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 420662009021 ParB-like nuclease domain; Region: ParB; smart00470 420662009022 ParB-like nuclease domain; Region: ParBc; cl02129 420662009023 RepB plasmid partitioning protein; Region: RepB; pfam07506 420662009024 Nuclease-related domain; Region: NERD; pfam08378 420662009025 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 420662009026 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 420662009027 active site 420662009028 DNA binding site [nucleotide binding] 420662009029 Int/Topo IB signature motif; other site 420662009030 Transposase domain (DUF772); Region: DUF772; pfam05598 420662009031 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662009032 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662009033 Transposase domain (DUF772); Region: DUF772; pfam05598 420662009034 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662009035 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662009036 Transposase domain (DUF772); Region: DUF772; pfam05598 420662009037 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662009038 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662009039 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 420662009040 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662009041 AAA domain; Region: AAA_23; pfam13476 420662009042 Walker A/P-loop; other site 420662009043 ATP binding site [chemical binding]; other site 420662009044 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 420662009045 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 420662009046 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 420662009047 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 420662009048 Walker A motif; other site 420662009049 ATP binding site [chemical binding]; other site 420662009050 Walker B motif; other site 420662009051 arginine finger; other site 420662009052 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 420662009053 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 420662009054 non-specific DNA binding site [nucleotide binding]; other site 420662009055 salt bridge; other site 420662009056 sequence-specific DNA binding site [nucleotide binding]; other site 420662009057 Integrase core domain; Region: rve; pfam00665 420662009058 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 420662009059 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 420662009060 active site 420662009061 DNA binding site [nucleotide binding] 420662009062 Int/Topo IB signature motif; other site 420662009063 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 420662009064 HemY protein N-terminus; Region: HemY_N; pfam07219 420662009065 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed; Region: PRK06975 420662009066 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 420662009067 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 420662009068 active site 420662009069 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; cl17708 420662009070 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 420662009071 domain interfaces; other site 420662009072 active site 420662009073 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 420662009074 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 420662009075 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 420662009076 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 420662009077 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 420662009078 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 420662009079 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 420662009080 catalytic core [active] 420662009081 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 420662009082 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 420662009083 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 420662009084 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 420662009085 putative domain interface [polypeptide binding]; other site 420662009086 putative active site [active] 420662009087 catalytic site [active] 420662009088 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 420662009089 putative domain interface [polypeptide binding]; other site 420662009090 putative active site [active] 420662009091 catalytic site [active] 420662009092 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662009093 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662009094 trimer interface [polypeptide binding]; other site 420662009095 eyelet of channel; other site 420662009096 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 420662009097 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 420662009098 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 420662009099 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 420662009100 putative active site [active] 420662009101 putative metal binding site [ion binding]; other site 420662009102 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 420662009103 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 420662009104 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 420662009105 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 420662009106 putative hydrophobic ligand binding site [chemical binding]; other site 420662009107 protein interface [polypeptide binding]; other site 420662009108 gate; other site 420662009109 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 420662009110 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 420662009111 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 420662009112 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 420662009113 Substrate-binding site [chemical binding]; other site 420662009114 Substrate specificity [chemical binding]; other site 420662009115 Protein of unknown function, DUF486; Region: DUF486; cl01236 420662009116 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 420662009117 catalytic center binding site [active] 420662009118 ATP binding site [chemical binding]; other site 420662009119 poly(A) polymerase; Region: pcnB; TIGR01942 420662009120 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 420662009121 active site 420662009122 NTP binding site [chemical binding]; other site 420662009123 metal binding triad [ion binding]; metal-binding site 420662009124 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 420662009125 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 420662009126 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 420662009127 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 420662009128 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 420662009129 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 420662009130 Walker A motif; other site 420662009131 ATP binding site [chemical binding]; other site 420662009132 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; cl17189 420662009133 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 420662009134 Domain of unknown function DUF20; Region: UPF0118; pfam01594 420662009135 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 420662009136 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 420662009137 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 420662009138 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 420662009139 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 420662009140 acetylornithine aminotransferase; Provisional; Region: PRK02627 420662009141 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 420662009142 inhibitor-cofactor binding pocket; inhibition site 420662009143 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662009144 catalytic residue [active] 420662009145 ornithine carbamoyltransferase; Provisional; Region: PRK00779 420662009146 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 420662009147 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 420662009148 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 420662009149 active site 420662009150 metal binding site [ion binding]; metal-binding site 420662009151 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 420662009152 Catalytic domain of Protein Kinases; Region: PKc; cd00180 420662009153 active site 420662009154 ATP binding site [chemical binding]; other site 420662009155 substrate binding site [chemical binding]; other site 420662009156 activation loop (A-loop); other site 420662009157 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 420662009158 Ligand Binding Site [chemical binding]; other site 420662009159 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 420662009160 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4430 420662009161 argininosuccinate synthase; Validated; Region: PRK05370 420662009162 argininosuccinate synthase; Provisional; Region: PRK13820 420662009163 Peptidase family M48; Region: Peptidase_M48; cl12018 420662009164 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 420662009165 FAD binding domain; Region: FAD_binding_4; pfam01565 420662009166 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 420662009167 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 420662009168 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 420662009169 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 420662009170 catalytic motif [active] 420662009171 Catalytic residue [active] 420662009172 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 420662009173 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 420662009174 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 420662009175 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 420662009176 active site 420662009177 uracil binding [chemical binding]; other site 420662009178 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662009179 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 420662009180 active site 420662009181 phosphorylation site [posttranslational modification] 420662009182 intermolecular recognition site; other site 420662009183 dimerization interface [polypeptide binding]; other site 420662009184 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 420662009185 DNA binding residues [nucleotide binding] 420662009186 dimerization interface [polypeptide binding]; other site 420662009187 HAMP domain; Region: HAMP; pfam00672 420662009188 dimerization interface [polypeptide binding]; other site 420662009189 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 420662009190 Histidine kinase; Region: HisKA_3; pfam07730 420662009191 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 420662009192 ATP binding site [chemical binding]; other site 420662009193 Mg2+ binding site [ion binding]; other site 420662009194 G-X-G motif; other site 420662009195 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 420662009196 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 420662009197 active site 420662009198 Riboflavin kinase; Region: Flavokinase; smart00904 420662009199 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 420662009200 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 420662009201 active site 420662009202 HIGH motif; other site 420662009203 nucleotide binding site [chemical binding]; other site 420662009204 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 420662009205 active site 420662009206 KMSKS motif; other site 420662009207 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 420662009208 tRNA binding surface [nucleotide binding]; other site 420662009209 anticodon binding site; other site 420662009210 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 420662009211 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 420662009212 lipoprotein signal peptidase; Provisional; Region: PRK14787 420662009213 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 420662009214 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 420662009215 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 420662009216 NADP binding site [chemical binding]; other site 420662009217 dimer interface [polypeptide binding]; other site 420662009218 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 420662009219 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662009220 EamA-like transporter family; Region: EamA; pfam00892 420662009221 PAS fold; Region: PAS_4; pfam08448 420662009222 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 420662009223 putative active site [active] 420662009224 heme pocket [chemical binding]; other site 420662009225 PAS domain S-box; Region: sensory_box; TIGR00229 420662009226 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 420662009227 putative active site [active] 420662009228 heme pocket [chemical binding]; other site 420662009229 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662009230 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662009231 metal binding site [ion binding]; metal-binding site 420662009232 active site 420662009233 I-site; other site 420662009234 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 420662009235 short chain dehydrogenase; Provisional; Region: PRK06125 420662009236 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662009237 NAD(P) binding site [chemical binding]; other site 420662009238 active site 420662009239 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662009240 EamA-like transporter family; Region: EamA; pfam00892 420662009241 EamA-like transporter family; Region: EamA; pfam00892 420662009242 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 420662009243 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 420662009244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 420662009245 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 420662009246 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 420662009247 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 420662009248 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 420662009249 Walker A motif; other site 420662009250 ATP binding site [chemical binding]; other site 420662009251 Walker B motif; other site 420662009252 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 420662009253 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 420662009254 active site 420662009255 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 420662009256 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 420662009257 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 420662009258 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 420662009259 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 420662009260 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 420662009261 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 420662009262 Rod binding protein; Region: Rod-binding; cl01626 420662009263 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 420662009264 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 420662009265 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 420662009266 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 420662009267 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 420662009268 Flagellar L-ring protein; Region: FlgH; pfam02107 420662009269 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 420662009270 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 420662009271 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 420662009272 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 420662009273 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 420662009274 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 420662009275 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 420662009276 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 420662009277 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 420662009278 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 420662009279 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 420662009280 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 420662009281 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 420662009282 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 420662009283 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 420662009284 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 420662009285 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 420662009286 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 420662009287 SAF-like; Region: SAF_2; pfam13144 420662009288 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 420662009289 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 420662009290 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 420662009291 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 420662009292 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 420662009293 FHIPEP family; Region: FHIPEP; pfam00771 420662009294 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 420662009295 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 420662009296 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 420662009297 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 420662009298 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 420662009299 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662009300 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 420662009301 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 420662009302 DNA binding residues [nucleotide binding] 420662009303 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662009304 acyltransferase, WS/DGAT/MGAT; Region: acyl_WS_DGAT; TIGR02946 420662009305 Wax ester synthase-like Acyl-CoA acyltransferase domain; Region: WES_acyltransf; pfam03007 420662009306 Protein of unknown function (DUF1298); Region: DUF1298; pfam06974 420662009307 Acyl CoA binding protein; Region: ACBP; pfam00887 420662009308 acyl-CoA binding pocket [chemical binding]; other site 420662009309 CoA binding site [chemical binding]; other site 420662009310 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; pfam09650 420662009311 Predicted aminopeptidase (DUF2265); Region: DUF2265; pfam10023 420662009312 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 420662009313 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 420662009314 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 420662009315 putative [4Fe-4S] binding site [ion binding]; other site 420662009316 putative molybdopterin cofactor binding site [chemical binding]; other site 420662009317 The MopB_CT_3 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_3; cd02786 420662009318 putative molybdopterin cofactor binding site; other site 420662009319 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 420662009320 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 420662009321 metal binding site [ion binding]; metal-binding site 420662009322 putative dimer interface [polypeptide binding]; other site 420662009323 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 420662009324 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 420662009325 motif II; other site 420662009326 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 420662009327 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 420662009328 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 420662009329 active site 420662009330 dimer interface [polypeptide binding]; other site 420662009331 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 420662009332 dimer interface [polypeptide binding]; other site 420662009333 active site 420662009334 transaldolase-like protein; Provisional; Region: PTZ00411 420662009335 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 420662009336 active site 420662009337 dimer interface [polypeptide binding]; other site 420662009338 catalytic residue [active] 420662009339 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 420662009340 anti sigma factor interaction site; other site 420662009341 regulatory phosphorylation site [posttranslational modification]; other site 420662009342 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 420662009343 VacJ like lipoprotein; Region: VacJ; cl01073 420662009344 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 420662009345 mce related protein; Region: MCE; pfam02470 420662009346 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 420662009347 Permease; Region: Permease; pfam02405 420662009348 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 420662009349 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 420662009350 Walker A/P-loop; other site 420662009351 ATP binding site [chemical binding]; other site 420662009352 Q-loop/lid; other site 420662009353 ABC transporter signature motif; other site 420662009354 Walker B; other site 420662009355 D-loop; other site 420662009356 H-loop/switch region; other site 420662009357 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 420662009358 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 420662009359 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 420662009360 active site 420662009361 dimer interface [polypeptide binding]; other site 420662009362 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 420662009363 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 420662009364 active site 420662009365 FMN binding site [chemical binding]; other site 420662009366 substrate binding site [chemical binding]; other site 420662009367 3Fe-4S cluster binding site [ion binding]; other site 420662009368 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 420662009369 domain interface; other site 420662009370 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662009371 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662009372 trimer interface [polypeptide binding]; other site 420662009373 eyelet of channel; other site 420662009374 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 420662009375 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 420662009376 Zn2+ binding site [ion binding]; other site 420662009377 Mg2+ binding site [ion binding]; other site 420662009378 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 420662009379 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 420662009380 active site 420662009381 dimer interface [polypeptide binding]; other site 420662009382 metal binding site [ion binding]; metal-binding site 420662009383 shikimate kinase; Reviewed; Region: aroK; PRK00131 420662009384 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 420662009385 ADP binding site [chemical binding]; other site 420662009386 magnesium binding site [ion binding]; other site 420662009387 putative shikimate binding site; other site 420662009388 AMIN domain; Region: AMIN; pfam11741 420662009389 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 420662009390 Secretin and TonB N terminus short domain; Region: STN; smart00965 420662009391 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 420662009392 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 420662009393 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 420662009394 Pilus assembly protein, PilP; Region: PilP; pfam04351 420662009395 Pilus assembly protein, PilO; Region: PilO; pfam04350 420662009396 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 420662009397 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 420662009398 Cell division protein FtsA; Region: FtsA; cl17206 420662009399 Competence protein A; Region: Competence_A; pfam11104 420662009400 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 420662009401 Transglycosylase; Region: Transgly; pfam00912 420662009402 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 420662009403 Frataxin-like domain; Region: Frataxin_Cyay; pfam01491 420662009404 putative iron binding site [ion binding]; other site 420662009405 diaminopimelate decarboxylase; Region: lysA; TIGR01048 420662009406 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 420662009407 active site 420662009408 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 420662009409 substrate binding site [chemical binding]; other site 420662009410 catalytic residues [active] 420662009411 dimer interface [polypeptide binding]; other site 420662009412 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 420662009413 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662009414 Walker A/P-loop; other site 420662009415 ATP binding site [chemical binding]; other site 420662009416 Q-loop/lid; other site 420662009417 ABC transporter signature motif; other site 420662009418 Walker B; other site 420662009419 D-loop; other site 420662009420 H-loop/switch region; other site 420662009421 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 420662009422 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 420662009423 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662009424 Walker A/P-loop; other site 420662009425 ATP binding site [chemical binding]; other site 420662009426 Q-loop/lid; other site 420662009427 ABC transporter signature motif; other site 420662009428 Walker B; other site 420662009429 D-loop; other site 420662009430 H-loop/switch region; other site 420662009431 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 420662009432 dipeptide transporter; Provisional; Region: PRK10913 420662009433 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 420662009434 dimer interface [polypeptide binding]; other site 420662009435 conserved gate region; other site 420662009436 putative PBP binding loops; other site 420662009437 ABC-ATPase subunit interface; other site 420662009438 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 420662009439 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 420662009440 dimer interface [polypeptide binding]; other site 420662009441 conserved gate region; other site 420662009442 putative PBP binding loops; other site 420662009443 ABC-ATPase subunit interface; other site 420662009444 Protein of unknown function (DUF3047); Region: DUF3047; pfam11249 420662009445 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 420662009446 trimer interface [polypeptide binding]; other site 420662009447 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 420662009448 eyelet of channel; other site 420662009449 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 420662009450 diiron binding motif [ion binding]; other site 420662009451 OsmC-like protein; Region: OsmC; cl00767 420662009452 threonine dehydratase; Reviewed; Region: PRK09224 420662009453 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 420662009454 tetramer interface [polypeptide binding]; other site 420662009455 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662009456 catalytic residue [active] 420662009457 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 420662009458 putative Ile/Val binding site [chemical binding]; other site 420662009459 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 420662009460 putative Ile/Val binding site [chemical binding]; other site 420662009461 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 420662009462 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 420662009463 putative dimer interface [polypeptide binding]; other site 420662009464 active site pocket [active] 420662009465 putative cataytic base [active] 420662009466 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 420662009467 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 420662009468 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 420662009469 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 420662009470 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 420662009471 GspL periplasmic domain; Region: GspL_C; cl14909 420662009472 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 420662009473 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 420662009474 type II secretion system protein D; Region: type_II_gspD; TIGR02517 420662009475 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 420662009476 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 420662009477 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 420662009478 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 420662009479 type II secretion system protein E; Region: type_II_gspE; TIGR02533 420662009480 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 420662009481 Walker A motif; other site 420662009482 ATP binding site [chemical binding]; other site 420662009483 Walker B motif; other site 420662009484 type II secretion system protein F; Region: GspF; TIGR02120 420662009485 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 420662009486 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 420662009487 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 420662009488 Walker A motif; other site 420662009489 ATP binding site [chemical binding]; other site 420662009490 Walker B motif; other site 420662009491 arginine finger; other site 420662009492 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 420662009493 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 420662009494 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 420662009495 putative active site [active] 420662009496 dimerization interface [polypeptide binding]; other site 420662009497 putative tRNAtyr binding site [nucleotide binding]; other site 420662009498 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 420662009499 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 420662009500 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 420662009501 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 420662009502 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 420662009503 active site 420662009504 phosphorylation site [posttranslational modification] 420662009505 intermolecular recognition site; other site 420662009506 dimerization interface [polypeptide binding]; other site 420662009507 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 420662009508 DNA binding site [nucleotide binding] 420662009509 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662009510 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 420662009511 ATP binding site [chemical binding]; other site 420662009512 Mg2+ binding site [ion binding]; other site 420662009513 G-X-G motif; other site 420662009514 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 420662009515 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 420662009516 active site 420662009517 HIGH motif; other site 420662009518 dimer interface [polypeptide binding]; other site 420662009519 KMSKS motif; other site 420662009520 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 420662009521 RNA binding surface [nucleotide binding]; other site 420662009522 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 420662009523 Peptidase family M23; Region: Peptidase_M23; pfam01551 420662009524 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 420662009525 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 420662009526 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 420662009527 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 420662009528 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 420662009529 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 420662009530 23S rRNA interface [nucleotide binding]; other site 420662009531 L3 interface [polypeptide binding]; other site 420662009532 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 420662009533 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662009534 Coenzyme A binding pocket [chemical binding]; other site 420662009535 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 420662009536 serine/threonine protein kinase; Provisional; Region: PRK11768 420662009537 Phosphotransferase enzyme family; Region: APH; pfam01636 420662009538 heat shock protein 90; Provisional; Region: PRK05218 420662009539 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 420662009540 ATP binding site [chemical binding]; other site 420662009541 Mg2+ binding site [ion binding]; other site 420662009542 G-X-G motif; other site 420662009543 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 420662009544 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 420662009545 Uncharacterized conserved protein [Function unknown]; Region: COG0011 420662009546 H-NS histone family; Region: Histone_HNS; pfam00816 420662009547 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 420662009548 GTP-binding protein YchF; Reviewed; Region: PRK09601 420662009549 YchF GTPase; Region: YchF; cd01900 420662009550 G1 box; other site 420662009551 GTP/Mg2+ binding site [chemical binding]; other site 420662009552 Switch I region; other site 420662009553 G2 box; other site 420662009554 Switch II region; other site 420662009555 G3 box; other site 420662009556 G4 box; other site 420662009557 G5 box; other site 420662009558 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 420662009559 MASE1; Region: MASE1; pfam05231 420662009560 CHASE domain; Region: CHASE; pfam03924 420662009561 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 420662009562 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 420662009563 putative active site [active] 420662009564 heme pocket [chemical binding]; other site 420662009565 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 420662009566 dimer interface [polypeptide binding]; other site 420662009567 phosphorylation site [posttranslational modification] 420662009568 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 420662009569 ATP binding site [chemical binding]; other site 420662009570 Mg2+ binding site [ion binding]; other site 420662009571 G-X-G motif; other site 420662009572 Response regulator receiver domain; Region: Response_reg; pfam00072 420662009573 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 420662009574 active site 420662009575 phosphorylation site [posttranslational modification] 420662009576 intermolecular recognition site; other site 420662009577 dimerization interface [polypeptide binding]; other site 420662009578 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 420662009579 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 420662009580 dimer interface [polypeptide binding]; other site 420662009581 phosphorylation site [posttranslational modification] 420662009582 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 420662009583 ATP binding site [chemical binding]; other site 420662009584 Mg2+ binding site [ion binding]; other site 420662009585 G-X-G motif; other site 420662009586 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 420662009587 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 420662009588 active site 420662009589 phosphorylation site [posttranslational modification] 420662009590 intermolecular recognition site; other site 420662009591 dimerization interface [polypeptide binding]; other site 420662009592 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 420662009593 DNA binding site [nucleotide binding] 420662009594 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 420662009595 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 420662009596 FAD binding site [chemical binding]; other site 420662009597 substrate binding pocket [chemical binding]; other site 420662009598 catalytic base [active] 420662009599 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 420662009600 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662009601 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 420662009602 DNA binding residues [nucleotide binding] 420662009603 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 420662009604 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 420662009605 Cu(I) binding site [ion binding]; other site 420662009606 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 420662009607 UbiA prenyltransferase family; Region: UbiA; pfam01040 420662009608 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 420662009609 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 420662009610 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 420662009611 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 420662009612 Subunit III/VIIa interface [polypeptide binding]; other site 420662009613 Phospholipid binding site [chemical binding]; other site 420662009614 Subunit I/III interface [polypeptide binding]; other site 420662009615 Subunit III/VIb interface [polypeptide binding]; other site 420662009616 Subunit III/VIa interface; other site 420662009617 Subunit III/Vb interface [polypeptide binding]; other site 420662009618 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 420662009619 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 420662009620 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 420662009621 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 420662009622 Subunit I/III interface [polypeptide binding]; other site 420662009623 D-pathway; other site 420662009624 Subunit I/VIIc interface [polypeptide binding]; other site 420662009625 Subunit I/IV interface [polypeptide binding]; other site 420662009626 Subunit I/II interface [polypeptide binding]; other site 420662009627 Low-spin heme (heme a) binding site [chemical binding]; other site 420662009628 Subunit I/VIIa interface [polypeptide binding]; other site 420662009629 Subunit I/VIa interface [polypeptide binding]; other site 420662009630 Dimer interface; other site 420662009631 Putative water exit pathway; other site 420662009632 Binuclear center (heme a3/CuB) [ion binding]; other site 420662009633 K-pathway; other site 420662009634 Subunit I/Vb interface [polypeptide binding]; other site 420662009635 Putative proton exit pathway; other site 420662009636 Subunit I/VIb interface; other site 420662009637 Subunit I/VIc interface [polypeptide binding]; other site 420662009638 Electron transfer pathway; other site 420662009639 Subunit I/VIIIb interface [polypeptide binding]; other site 420662009640 Subunit I/VIIb interface [polypeptide binding]; other site 420662009641 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 420662009642 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 420662009643 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 420662009644 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 420662009645 Cytochrome c; Region: Cytochrom_C; pfam00034 420662009646 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 420662009647 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 420662009648 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 420662009649 S-adenosylmethionine binding site [chemical binding]; other site 420662009650 DNA utilization protein GntX; Provisional; Region: PRK11595 420662009651 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662009652 active site 420662009653 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 420662009654 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 420662009655 putative binding surface; other site 420662009656 active site 420662009657 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 420662009658 putative binding surface; other site 420662009659 active site 420662009660 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 420662009661 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 420662009662 ATP binding site [chemical binding]; other site 420662009663 Mg2+ binding site [ion binding]; other site 420662009664 G-X-G motif; other site 420662009665 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 420662009666 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 420662009667 Response regulator receiver domain; Region: Response_reg; pfam00072 420662009668 active site 420662009669 phosphorylation site [posttranslational modification] 420662009670 intermolecular recognition site; other site 420662009671 dimerization interface [polypeptide binding]; other site 420662009672 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 420662009673 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 420662009674 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662009675 dimer interface [polypeptide binding]; other site 420662009676 putative CheW interface [polypeptide binding]; other site 420662009677 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 420662009678 Response regulator receiver domain; Region: Response_reg; pfam00072 420662009679 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 420662009680 active site 420662009681 phosphorylation site [posttranslational modification] 420662009682 intermolecular recognition site; other site 420662009683 dimerization interface [polypeptide binding]; other site 420662009684 Response regulator receiver domain; Region: Response_reg; pfam00072 420662009685 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 420662009686 active site 420662009687 phosphorylation site [posttranslational modification] 420662009688 intermolecular recognition site; other site 420662009689 dimerization interface [polypeptide binding]; other site 420662009690 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 420662009691 Rubredoxin; Region: Rubredoxin; pfam00301 420662009692 iron binding site [ion binding]; other site 420662009693 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 420662009694 dimer interface [polypeptide binding]; other site 420662009695 substrate binding site [chemical binding]; other site 420662009696 ATP binding site [chemical binding]; other site 420662009697 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 420662009698 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 420662009699 inhibitor-cofactor binding pocket; inhibition site 420662009700 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662009701 catalytic residue [active] 420662009702 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 420662009703 active site 420662009704 phosphate binding residues; other site 420662009705 catalytic residues [active] 420662009706 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 420662009707 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 420662009708 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662009709 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662009710 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 420662009711 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662009712 Exoribonuclease R [Transcription]; Region: VacB; COG0557 420662009713 RNB domain; Region: RNB; pfam00773 420662009714 TonB C terminal; Region: TonB_2; pfam13103 420662009715 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 420662009716 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 420662009717 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 420662009718 NAD(P) binding site [chemical binding]; other site 420662009719 shikimate binding site; other site 420662009720 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 420662009721 Transglycosylase; Region: Transgly; cl17702 420662009722 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 420662009723 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662009724 catalytic residues [active] 420662009725 Dehydroquinase class II; Region: DHquinase_II; pfam01220 420662009726 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 420662009727 trimer interface [polypeptide binding]; other site 420662009728 active site 420662009729 dimer interface [polypeptide binding]; other site 420662009730 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 420662009731 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 420662009732 carboxyltransferase (CT) interaction site; other site 420662009733 biotinylation site [posttranslational modification]; other site 420662009734 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 420662009735 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 420662009736 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 420662009737 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 420662009738 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 420662009739 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 420662009740 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 420662009741 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 420662009742 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 420662009743 substrate binding site [chemical binding]; other site 420662009744 ATP binding site [chemical binding]; other site 420662009745 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 420662009746 dimer interface [polypeptide binding]; other site 420662009747 putative radical transfer pathway; other site 420662009748 diiron center [ion binding]; other site 420662009749 tyrosyl radical; other site 420662009750 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 420662009751 ATP cone domain; Region: ATP-cone; pfam03477 420662009752 ATP cone domain; Region: ATP-cone; pfam03477 420662009753 Class I ribonucleotide reductase; Region: RNR_I; cd01679 420662009754 active site 420662009755 dimer interface [polypeptide binding]; other site 420662009756 catalytic residues [active] 420662009757 effector binding site; other site 420662009758 R2 peptide binding site; other site 420662009759 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 420662009760 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 420662009761 amidase catalytic site [active] 420662009762 Zn binding residues [ion binding]; other site 420662009763 substrate binding site [chemical binding]; other site 420662009764 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 420662009765 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 420662009766 active site 420662009767 phosphorylation site [posttranslational modification] 420662009768 intermolecular recognition site; other site 420662009769 dimerization interface [polypeptide binding]; other site 420662009770 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 420662009771 Walker A motif; other site 420662009772 ATP binding site [chemical binding]; other site 420662009773 Walker B motif; other site 420662009774 arginine finger; other site 420662009775 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662009776 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662009777 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 420662009778 dimer interface [polypeptide binding]; other site 420662009779 phosphorylation site [posttranslational modification] 420662009780 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 420662009781 ATP binding site [chemical binding]; other site 420662009782 Mg2+ binding site [ion binding]; other site 420662009783 G-X-G motif; other site 420662009784 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 420662009785 signal recognition particle protein; Provisional; Region: PRK10867 420662009786 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 420662009787 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 420662009788 P loop; other site 420662009789 GTP binding site [chemical binding]; other site 420662009790 Signal peptide binding domain; Region: SRP_SPB; pfam02978 420662009791 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 420662009792 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 420662009793 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 420662009794 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 420662009795 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 420662009796 S-adenosylmethionine binding site [chemical binding]; other site 420662009797 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 420662009798 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 420662009799 active site 420662009800 (T/H)XGH motif; other site 420662009801 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 420662009802 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 420662009803 putative active site [active] 420662009804 catalytic residue [active] 420662009805 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 420662009806 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 420662009807 5S rRNA interface [nucleotide binding]; other site 420662009808 CTC domain interface [polypeptide binding]; other site 420662009809 L16 interface [polypeptide binding]; other site 420662009810 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 420662009811 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 420662009812 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662009813 active site 420662009814 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 420662009815 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 420662009816 TPR repeat; Region: TPR_11; pfam13414 420662009817 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 420662009818 binding surface 420662009819 TPR motif; other site 420662009820 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 420662009821 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 420662009822 DNA binding site [nucleotide binding] 420662009823 catalytic residue [active] 420662009824 H2TH interface [polypeptide binding]; other site 420662009825 putative catalytic residues [active] 420662009826 turnover-facilitating residue; other site 420662009827 intercalation triad [nucleotide binding]; other site 420662009828 8OG recognition residue [nucleotide binding]; other site 420662009829 putative reading head residues; other site 420662009830 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 420662009831 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 420662009832 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 420662009833 G1 box; other site 420662009834 GTP/Mg2+ binding site [chemical binding]; other site 420662009835 G2 box; other site 420662009836 Switch I region; other site 420662009837 G3 box; other site 420662009838 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 420662009839 G3 box; other site 420662009840 Switch II region; other site 420662009841 GTP/Mg2+ binding site [chemical binding]; other site 420662009842 G4 box; other site 420662009843 G5 box; other site 420662009844 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 420662009845 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 420662009846 minor groove reading motif; other site 420662009847 helix-hairpin-helix signature motif; other site 420662009848 substrate binding pocket [chemical binding]; other site 420662009849 active site 420662009850 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 420662009851 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 420662009852 DNA binding and oxoG recognition site [nucleotide binding] 420662009853 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 420662009854 RuvA N terminal domain; Region: RuvA_N; pfam01330 420662009855 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 420662009856 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662009857 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 420662009858 active site 420662009859 phosphorylation site [posttranslational modification] 420662009860 intermolecular recognition site; other site 420662009861 dimerization interface [polypeptide binding]; other site 420662009862 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 420662009863 DNA binding residues [nucleotide binding] 420662009864 dimerization interface [polypeptide binding]; other site 420662009865 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 420662009866 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 420662009867 Histidine kinase; Region: HisKA_3; pfam07730 420662009868 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 420662009869 ATP binding site [chemical binding]; other site 420662009870 Mg2+ binding site [ion binding]; other site 420662009871 G-X-G motif; other site 420662009872 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 420662009873 PhoH-like protein; Region: PhoH; pfam02562 420662009874 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 420662009875 Ion channel; Region: Ion_trans_2; pfam07885 420662009876 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 420662009877 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 420662009878 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 420662009879 putative RNA binding site [nucleotide binding]; other site 420662009880 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 420662009881 S-adenosylmethionine binding site [chemical binding]; other site 420662009882 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 420662009883 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 420662009884 active site 420662009885 DNA binding site [nucleotide binding] 420662009886 Int/Topo IB signature motif; other site 420662009887 Protein of unknown function, DUF484; Region: DUF484; cl17449 420662009888 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 420662009889 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 420662009890 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 420662009891 Methyltransferase domain; Region: Methyltransf_31; pfam13847 420662009892 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 420662009893 S-adenosylmethionine binding site [chemical binding]; other site 420662009894 Nitronate monooxygenase; Region: NMO; pfam03060 420662009895 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 420662009896 FMN binding site [chemical binding]; other site 420662009897 substrate binding site [chemical binding]; other site 420662009898 putative catalytic residue [active] 420662009899 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662009900 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 420662009901 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 420662009902 SAF domain of putative dehydrogenases or oxidoreductases; Region: SAF_DH_OX_like; cd11616 420662009903 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 420662009904 putative acyl-acceptor binding pocket; other site 420662009905 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 420662009906 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 420662009907 putative acyl-acceptor binding pocket; other site 420662009908 S-adenosylmethionine synthetase; Validated; Region: PRK05250 420662009909 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 420662009910 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 420662009911 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 420662009912 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662009913 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662009914 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 420662009915 putative dimerization interface [polypeptide binding]; other site 420662009916 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 420662009917 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 420662009918 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 420662009919 CoA binding domain; Region: CoA_binding; smart00881 420662009920 CoA-ligase; Region: Ligase_CoA; pfam00549 420662009921 malate--CoA ligase subunit beta; Provisional; Region: PRK14046 420662009922 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 420662009923 CoA-ligase; Region: Ligase_CoA; pfam00549 420662009924 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 420662009925 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 420662009926 NADP binding domain of methylene tetrahydromethanopterin dehydrogenase; Region: NAD_bind_H4MPT_DH; cd01078 420662009927 NADP binding site [chemical binding]; other site 420662009928 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 420662009929 glycerate dehydrogenase; Provisional; Region: PRK06487 420662009930 putative ligand binding site [chemical binding]; other site 420662009931 putative NAD binding site [chemical binding]; other site 420662009932 catalytic site [active] 420662009933 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 420662009934 homodimer interface [polypeptide binding]; other site 420662009935 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662009936 catalytic residue [active] 420662009937 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 420662009938 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 420662009939 dimer interface [polypeptide binding]; other site 420662009940 active site 420662009941 glycine-pyridoxal phosphate binding site [chemical binding]; other site 420662009942 folate binding site [chemical binding]; other site 420662009943 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 420662009944 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 420662009945 MOFRL family; Region: MOFRL; pfam05161 420662009946 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 420662009947 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 420662009948 Potassium binding sites [ion binding]; other site 420662009949 Cesium cation binding sites [ion binding]; other site 420662009950 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 420662009951 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 420662009952 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 420662009953 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 420662009954 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 420662009955 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 420662009956 N-terminal plug; other site 420662009957 ligand-binding site [chemical binding]; other site 420662009958 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 420662009959 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 420662009960 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 420662009961 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 420662009962 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 420662009963 metal ion-dependent adhesion site (MIDAS); other site 420662009964 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 420662009965 metal ion-dependent adhesion site (MIDAS); other site 420662009966 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 420662009967 MoxR-like ATPases [General function prediction only]; Region: COG0714 420662009968 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 420662009969 Walker A motif; other site 420662009970 ATP binding site [chemical binding]; other site 420662009971 Walker B motif; other site 420662009972 arginine finger; other site 420662009973 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 420662009974 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662009975 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 420662009976 FAD binding domain; Region: FAD_binding_3; pfam01494 420662009977 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662009978 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 420662009979 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 420662009980 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 420662009981 G1 box; other site 420662009982 putative GEF interaction site [polypeptide binding]; other site 420662009983 GTP/Mg2+ binding site [chemical binding]; other site 420662009984 Switch I region; other site 420662009985 G2 box; other site 420662009986 G3 box; other site 420662009987 Switch II region; other site 420662009988 G4 box; other site 420662009989 G5 box; other site 420662009990 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 420662009991 transcriptional regulator; Provisional; Region: PRK10632 420662009992 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_2; cd08471 420662009993 putative effector binding pocket; other site 420662009994 putative dimerization interface [polypeptide binding]; other site 420662009995 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662009996 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 420662009997 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662009998 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 420662009999 putative C-terminal domain interface [polypeptide binding]; other site 420662010000 putative GSH binding site (G-site) [chemical binding]; other site 420662010001 putative dimer interface [polypeptide binding]; other site 420662010002 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 420662010003 putative N-terminal domain interface [polypeptide binding]; other site 420662010004 putative dimer interface [polypeptide binding]; other site 420662010005 putative substrate binding pocket (H-site) [chemical binding]; other site 420662010006 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 420662010007 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 420662010008 homotetramer interface [polypeptide binding]; other site 420662010009 ligand binding site [chemical binding]; other site 420662010010 catalytic site [active] 420662010011 NAD binding site [chemical binding]; other site 420662010012 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 420662010013 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 420662010014 RNA binding surface [nucleotide binding]; other site 420662010015 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 420662010016 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 420662010017 FAD binding site [chemical binding]; other site 420662010018 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 420662010019 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 420662010020 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 420662010021 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 420662010022 TfoX N-terminal domain; Region: TfoX_N; pfam04993 420662010023 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 420662010024 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 420662010025 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662010026 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 420662010027 dimerization interface [polypeptide binding]; other site 420662010028 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 420662010029 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 420662010030 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662010031 catalytic residue [active] 420662010032 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 420662010033 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 420662010034 putative NAD(P) binding site [chemical binding]; other site 420662010035 active site 420662010036 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 420662010037 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662010038 putative C-terminal domain interface [polypeptide binding]; other site 420662010039 putative GSH binding site (G-site) [chemical binding]; other site 420662010040 putative dimer interface [polypeptide binding]; other site 420662010041 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 420662010042 putative N-terminal domain interface [polypeptide binding]; other site 420662010043 putative dimer interface [polypeptide binding]; other site 420662010044 putative substrate binding pocket (H-site) [chemical binding]; other site 420662010045 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 420662010046 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 420662010047 active site 420662010048 NTP binding site [chemical binding]; other site 420662010049 metal binding triad [ion binding]; metal-binding site 420662010050 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 420662010051 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662010052 putative CheW interface [polypeptide binding]; other site 420662010053 SnoaL-like domain; Region: SnoaL_2; pfam12680 420662010054 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662010055 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 420662010056 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 420662010057 Walker A motif; other site 420662010058 ATP binding site [chemical binding]; other site 420662010059 Walker B motif; other site 420662010060 arginine finger; other site 420662010061 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 420662010062 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 420662010063 non-specific DNA binding site [nucleotide binding]; other site 420662010064 salt bridge; other site 420662010065 sequence-specific DNA binding site [nucleotide binding]; other site 420662010066 Integrase core domain; Region: rve; pfam00665 420662010067 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 420662010068 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 420662010069 dimerization interface [polypeptide binding]; other site 420662010070 putative path to active site cavity [active] 420662010071 diiron center [ion binding]; other site 420662010072 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 420662010073 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 420662010074 dimerization interface [polypeptide binding]; other site 420662010075 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 420662010076 Activator of aromatic catabolism; Region: XylR_N; pfam06505 420662010077 The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons; Region: V4R; smart00989 420662010078 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 420662010079 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 420662010080 Walker A motif; other site 420662010081 ATP binding site [chemical binding]; other site 420662010082 Walker B motif; other site 420662010083 arginine finger; other site 420662010084 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 420662010085 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 420662010086 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 420662010087 tetramer interface [polypeptide binding]; other site 420662010088 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 420662010089 tetramer interface [polypeptide binding]; other site 420662010090 active site 420662010091 Fe binding site [ion binding]; other site 420662010092 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 420662010093 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662010094 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_Chlorocatechol; cd08446 420662010095 dimerization interface [polypeptide binding]; other site 420662010096 putative substrate binding pocket [chemical binding]; other site 420662010097 DTW domain; Region: DTW; cl01221 420662010098 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 420662010099 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 420662010100 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662010101 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662010102 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_2; cd08471 420662010103 putative effector binding pocket; other site 420662010104 putative dimerization interface [polypeptide binding]; other site 420662010105 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 420662010106 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 420662010107 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 420662010108 classical (c) SDRs; Region: SDR_c; cd05233 420662010109 NAD(P) binding site [chemical binding]; other site 420662010110 active site 420662010111 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 420662010112 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 420662010113 active site 420662010114 catalytic residues [active] 420662010115 metal binding site [ion binding]; metal-binding site 420662010116 DmpG-like communication domain; Region: DmpG_comm; pfam07836 420662010117 acetaldehyde dehydrogenase; Validated; Region: PRK08300 420662010118 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 420662010119 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 420662010120 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 420662010121 active site 1 [active] 420662010122 dimer interface [polypeptide binding]; other site 420662010123 hexamer interface [polypeptide binding]; other site 420662010124 active site 2 [active] 420662010125 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 420662010126 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 420662010127 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 420662010128 NAD(P) binding site [chemical binding]; other site 420662010129 catalytic residues [active] 420662010130 Transposase domain (DUF772); Region: DUF772; pfam05598 420662010131 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662010132 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662010133 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 420662010134 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 420662010135 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662010136 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662010137 metal binding site [ion binding]; metal-binding site 420662010138 active site 420662010139 I-site; other site 420662010140 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 420662010141 HipA N-terminal domain; Region: couple_hipA; TIGR03071 420662010142 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 420662010143 HipA-like N-terminal domain; Region: HipA_N; pfam07805 420662010144 HipA-like C-terminal domain; Region: HipA_C; pfam07804 420662010145 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 420662010146 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 420662010147 non-specific DNA binding site [nucleotide binding]; other site 420662010148 salt bridge; other site 420662010149 sequence-specific DNA binding site [nucleotide binding]; other site 420662010150 fumarate hydratase; Reviewed; Region: fumC; PRK00485 420662010151 Class II fumarases; Region: Fumarase_classII; cd01362 420662010152 active site 420662010153 tetramer interface [polypeptide binding]; other site 420662010154 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 420662010155 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 420662010156 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 420662010157 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 420662010158 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 420662010159 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 420662010160 Walker A/P-loop; other site 420662010161 ATP binding site [chemical binding]; other site 420662010162 Q-loop/lid; other site 420662010163 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 420662010164 Q-loop/lid; other site 420662010165 ABC transporter signature motif; other site 420662010166 Walker B; other site 420662010167 D-loop; other site 420662010168 H-loop/switch region; other site 420662010169 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 420662010170 AAA domain; Region: AAA_18; pfam13238 420662010171 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 420662010172 tyrosine decarboxylase; Region: PLN02880 420662010173 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 420662010174 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662010175 catalytic residue [active] 420662010176 Uncharacterized conserved protein [Function unknown]; Region: COG1284 420662010177 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 420662010178 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662010179 GAF domain; Region: GAF; pfam01590 420662010180 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 420662010181 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 420662010182 cell division topological specificity factor MinE; Provisional; Region: PRK13989 420662010183 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 420662010184 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 420662010185 Switch I; other site 420662010186 Switch II; other site 420662010187 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 420662010188 septum formation inhibitor; Reviewed; Region: PRK01973 420662010189 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 420662010190 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 420662010191 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 420662010192 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 420662010193 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662010194 Walker A/P-loop; other site 420662010195 ATP binding site [chemical binding]; other site 420662010196 Q-loop/lid; other site 420662010197 ABC transporter signature motif; other site 420662010198 Walker B; other site 420662010199 D-loop; other site 420662010200 H-loop/switch region; other site 420662010201 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 420662010202 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662010203 Walker A/P-loop; other site 420662010204 ATP binding site [chemical binding]; other site 420662010205 Q-loop/lid; other site 420662010206 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 420662010207 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 420662010208 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 420662010209 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 420662010210 active site 420662010211 catalytic site [active] 420662010212 substrate binding site [chemical binding]; other site 420662010213 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 420662010214 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 420662010215 ligand binding site [chemical binding]; other site 420662010216 flexible hinge region; other site 420662010217 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 420662010218 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 420662010219 metal binding triad; other site 420662010220 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 420662010221 putative substrate translocation pore; other site 420662010222 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 420662010223 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 420662010224 putative catalytic residue [active] 420662010225 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 420662010226 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 420662010227 putative deacylase active site [active] 420662010228 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 420662010229 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 420662010230 active site 420662010231 catalytic residues [active] 420662010232 metal binding site [ion binding]; metal-binding site 420662010233 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 420662010234 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 420662010235 ATP-grasp domain; Region: ATP-grasp_4; cl17255 420662010236 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 420662010237 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 420662010238 carboxyltransferase (CT) interaction site; other site 420662010239 biotinylation site [posttranslational modification]; other site 420662010240 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 420662010241 enoyl-CoA hydratase; Provisional; Region: PRK05995 420662010242 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 420662010243 substrate binding site [chemical binding]; other site 420662010244 oxyanion hole (OAH) forming residues; other site 420662010245 trimer interface [polypeptide binding]; other site 420662010246 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 420662010247 isovaleryl-CoA dehydrogenase; Region: PLN02519 420662010248 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 420662010249 substrate binding site [chemical binding]; other site 420662010250 FAD binding site [chemical binding]; other site 420662010251 catalytic base [active] 420662010252 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662010253 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662010254 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 420662010255 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 420662010256 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 420662010257 putative catalytic residue [active] 420662010258 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 420662010259 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 420662010260 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 420662010261 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 420662010262 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 420662010263 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 420662010264 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 420662010265 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 420662010266 dimer interface [polypeptide binding]; other site 420662010267 active site 420662010268 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 420662010269 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 420662010270 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 420662010271 active site clefts [active] 420662010272 zinc binding site [ion binding]; other site 420662010273 dimer interface [polypeptide binding]; other site 420662010274 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662010275 Transcriptional regulators [Transcription]; Region: GntR; COG1802 420662010276 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662010277 DNA-binding site [nucleotide binding]; DNA binding site 420662010278 FCD domain; Region: FCD; cl11656 420662010279 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 420662010280 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 420662010281 dimer interface [polypeptide binding]; other site 420662010282 conserved gate region; other site 420662010283 ABC-ATPase subunit interface; other site 420662010284 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 420662010285 dimer interface [polypeptide binding]; other site 420662010286 conserved gate region; other site 420662010287 putative PBP binding loops; other site 420662010288 ABC-ATPase subunit interface; other site 420662010289 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 420662010290 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 420662010291 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 420662010292 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662010293 Walker A/P-loop; other site 420662010294 ATP binding site [chemical binding]; other site 420662010295 Q-loop/lid; other site 420662010296 ABC transporter signature motif; other site 420662010297 Walker B; other site 420662010298 D-loop; other site 420662010299 H-loop/switch region; other site 420662010300 TOBE domain; Region: TOBE_2; pfam08402 420662010301 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 420662010302 Protein of unknown function DUF45; Region: DUF45; pfam01863 420662010303 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 420662010304 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 420662010305 putative acyl-acceptor binding pocket; other site 420662010306 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 420662010307 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 420662010308 active site 420662010309 motif I; other site 420662010310 motif II; other site 420662010311 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 420662010312 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 420662010313 dimer interface [polypeptide binding]; other site 420662010314 motif 1; other site 420662010315 active site 420662010316 motif 2; other site 420662010317 motif 3; other site 420662010318 Cytochrome P450; Region: p450; pfam00067 420662010319 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 420662010320 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 420662010321 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 420662010322 putative active site [active] 420662010323 catalytic triad [active] 420662010324 putative dimer interface [polypeptide binding]; other site 420662010325 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 420662010326 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 420662010327 Transporter associated domain; Region: CorC_HlyC; smart01091 420662010328 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 420662010329 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 420662010330 P-loop, Walker A motif; other site 420662010331 Base recognition motif; other site 420662010332 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 420662010333 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 420662010334 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 420662010335 ATP-dependent protease subunit HslV; Provisional; Region: PRK05456 420662010336 active site 420662010337 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 420662010338 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 420662010339 Walker A motif; other site 420662010340 ATP binding site [chemical binding]; other site 420662010341 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 420662010342 Walker B motif; other site 420662010343 arginine finger; other site 420662010344 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 420662010345 pantothenate kinase; Reviewed; Region: PRK13329 420662010346 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662010347 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 420662010348 Trp docking motif [polypeptide binding]; other site 420662010349 dimer interface [polypeptide binding]; other site 420662010350 active site 420662010351 small subunit binding site [polypeptide binding]; other site 420662010352 c-type cytochrome, methanol metabolism-related; Region: 4cys_cytochr; TIGR03874 420662010353 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein; Region: ABC_peri_MoxJ_2; TIGR03871 420662010354 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 420662010355 substrate binding pocket [chemical binding]; other site 420662010356 membrane-bound complex binding site; other site 420662010357 hinge residues; other site 420662010358 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 420662010359 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662010360 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 420662010361 TPR repeat; Region: TPR_11; pfam13414 420662010362 binding surface 420662010363 TPR motif; other site 420662010364 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 420662010365 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 420662010366 Major Facilitator Superfamily; Region: MFS_1; pfam07690 420662010367 putative substrate translocation pore; other site 420662010368 AMP nucleosidase; Provisional; Region: PRK08292 420662010369 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 420662010370 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 420662010371 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 420662010372 elongation factor G; Reviewed; Region: PRK12740 420662010373 G1 box; other site 420662010374 putative GEF interaction site [polypeptide binding]; other site 420662010375 GTP/Mg2+ binding site [chemical binding]; other site 420662010376 Switch I region; other site 420662010377 G2 box; other site 420662010378 G3 box; other site 420662010379 Switch II region; other site 420662010380 G4 box; other site 420662010381 G5 box; other site 420662010382 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 420662010383 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 420662010384 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 420662010385 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 420662010386 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 420662010387 Type II transport protein GspH; Region: GspH; pfam12019 420662010388 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 420662010389 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 420662010390 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 420662010391 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 420662010392 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 420662010393 HDOD domain; Region: HDOD; pfam08668 420662010394 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 420662010395 S-adenosylmethionine binding site [chemical binding]; other site 420662010396 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 420662010397 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 420662010398 XdhC Rossmann domain; Region: XdhC_C; pfam13478 420662010399 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 420662010400 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662010401 Walker A/P-loop; other site 420662010402 ATP binding site [chemical binding]; other site 420662010403 Q-loop/lid; other site 420662010404 ABC transporter signature motif; other site 420662010405 Walker B; other site 420662010406 D-loop; other site 420662010407 H-loop/switch region; other site 420662010408 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662010409 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 420662010410 putative PBP binding loops; other site 420662010411 ABC-ATPase subunit interface; other site 420662010412 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 420662010413 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 420662010414 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 420662010415 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 420662010416 DsbD alpha interface [polypeptide binding]; other site 420662010417 catalytic residues [active] 420662010418 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 420662010419 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 420662010420 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 420662010421 alphaNTD - beta interaction site [polypeptide binding]; other site 420662010422 alphaNTD homodimer interface [polypeptide binding]; other site 420662010423 alphaNTD - beta' interaction site [polypeptide binding]; other site 420662010424 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 420662010425 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 420662010426 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 420662010427 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 420662010428 RNA binding surface [nucleotide binding]; other site 420662010429 30S ribosomal protein S11; Validated; Region: PRK05309 420662010430 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 420662010431 30S ribosomal protein S13; Region: bact_S13; TIGR03631 420662010432 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 420662010433 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 420662010434 rRNA binding site [nucleotide binding]; other site 420662010435 predicted 30S ribosome binding site; other site 420662010436 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 420662010437 SecY translocase; Region: SecY; pfam00344 420662010438 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 420662010439 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 420662010440 23S rRNA binding site [nucleotide binding]; other site 420662010441 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 420662010442 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 420662010443 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 420662010444 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 420662010445 5S rRNA interface [nucleotide binding]; other site 420662010446 L27 interface [polypeptide binding]; other site 420662010447 23S rRNA interface [nucleotide binding]; other site 420662010448 L5 interface [polypeptide binding]; other site 420662010449 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 420662010450 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 420662010451 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 420662010452 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 420662010453 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 420662010454 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 420662010455 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 420662010456 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 420662010457 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 420662010458 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 420662010459 catalytic triad [active] 420662010460 dimer interface [polypeptide binding]; other site 420662010461 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 420662010462 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 420662010463 23S rRNA interface [nucleotide binding]; other site 420662010464 putative translocon interaction site; other site 420662010465 signal recognition particle (SRP54) interaction site; other site 420662010466 L23 interface [polypeptide binding]; other site 420662010467 trigger factor interaction site; other site 420662010468 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 420662010469 23S rRNA interface [nucleotide binding]; other site 420662010470 5S rRNA interface [nucleotide binding]; other site 420662010471 putative antibiotic binding site [chemical binding]; other site 420662010472 L25 interface [polypeptide binding]; other site 420662010473 L27 interface [polypeptide binding]; other site 420662010474 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 420662010475 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 420662010476 G-X-X-G motif; other site 420662010477 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 420662010478 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 420662010479 putative translocon binding site; other site 420662010480 protein-rRNA interface [nucleotide binding]; other site 420662010481 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 420662010482 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 420662010483 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 420662010484 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 420662010485 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 420662010486 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 420662010487 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 420662010488 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 420662010489 elongation factor Tu; Reviewed; Region: PRK00049 420662010490 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 420662010491 G1 box; other site 420662010492 GEF interaction site [polypeptide binding]; other site 420662010493 GTP/Mg2+ binding site [chemical binding]; other site 420662010494 Switch I region; other site 420662010495 G2 box; other site 420662010496 G3 box; other site 420662010497 Switch II region; other site 420662010498 G4 box; other site 420662010499 G5 box; other site 420662010500 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 420662010501 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 420662010502 Antibiotic Binding Site [chemical binding]; other site 420662010503 elongation factor G; Reviewed; Region: PRK00007 420662010504 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 420662010505 G1 box; other site 420662010506 putative GEF interaction site [polypeptide binding]; other site 420662010507 GTP/Mg2+ binding site [chemical binding]; other site 420662010508 Switch I region; other site 420662010509 G2 box; other site 420662010510 G3 box; other site 420662010511 Switch II region; other site 420662010512 G4 box; other site 420662010513 G5 box; other site 420662010514 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 420662010515 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 420662010516 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 420662010517 30S ribosomal protein S7; Validated; Region: PRK05302 420662010518 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 420662010519 S17 interaction site [polypeptide binding]; other site 420662010520 S8 interaction site; other site 420662010521 16S rRNA interaction site [nucleotide binding]; other site 420662010522 streptomycin interaction site [chemical binding]; other site 420662010523 23S rRNA interaction site [nucleotide binding]; other site 420662010524 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 420662010525 PIN domain; Region: PIN_3; pfam13470 420662010526 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 420662010527 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 420662010528 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 420662010529 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 420662010530 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 420662010531 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 420662010532 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 420662010533 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 420662010534 Apocytochrome F, C-terminal; Region: Apocytochr_F_C; cl03168 420662010535 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 420662010536 DNA binding site [nucleotide binding] 420662010537 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 420662010538 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 420662010539 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 420662010540 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 420662010541 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 420662010542 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 420662010543 RPB3 interaction site [polypeptide binding]; other site 420662010544 RPB1 interaction site [polypeptide binding]; other site 420662010545 RPB11 interaction site [polypeptide binding]; other site 420662010546 RPB10 interaction site [polypeptide binding]; other site 420662010547 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 420662010548 peripheral dimer interface [polypeptide binding]; other site 420662010549 core dimer interface [polypeptide binding]; other site 420662010550 L10 interface [polypeptide binding]; other site 420662010551 L11 interface [polypeptide binding]; other site 420662010552 putative EF-Tu interaction site [polypeptide binding]; other site 420662010553 putative EF-G interaction site [polypeptide binding]; other site 420662010554 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 420662010555 23S rRNA interface [nucleotide binding]; other site 420662010556 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 420662010557 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 420662010558 mRNA/rRNA interface [nucleotide binding]; other site 420662010559 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 420662010560 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 420662010561 23S rRNA interface [nucleotide binding]; other site 420662010562 L7/L12 interface [polypeptide binding]; other site 420662010563 putative thiostrepton binding site; other site 420662010564 L25 interface [polypeptide binding]; other site 420662010565 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 420662010566 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 420662010567 putative homodimer interface [polypeptide binding]; other site 420662010568 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 420662010569 heterodimer interface [polypeptide binding]; other site 420662010570 homodimer interface [polypeptide binding]; other site 420662010571 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 420662010572 elongation factor Tu; Reviewed; Region: PRK00049 420662010573 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 420662010574 G1 box; other site 420662010575 GEF interaction site [polypeptide binding]; other site 420662010576 GTP/Mg2+ binding site [chemical binding]; other site 420662010577 Switch I region; other site 420662010578 G2 box; other site 420662010579 G3 box; other site 420662010580 Switch II region; other site 420662010581 G4 box; other site 420662010582 G5 box; other site 420662010583 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 420662010584 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 420662010585 Antibiotic Binding Site [chemical binding]; other site 420662010586 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 420662010587 ligand binding site [chemical binding]; other site 420662010588 active site 420662010589 UGI interface [polypeptide binding]; other site 420662010590 catalytic site [active] 420662010591 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 420662010592 active site 420662010593 ribulose/triose binding site [chemical binding]; other site 420662010594 phosphate binding site [ion binding]; other site 420662010595 substrate (anthranilate) binding pocket [chemical binding]; other site 420662010596 product (indole) binding pocket [chemical binding]; other site 420662010597 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 420662010598 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 420662010599 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 420662010600 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 420662010601 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 420662010602 glutamine binding [chemical binding]; other site 420662010603 catalytic triad [active] 420662010604 anthranilate synthase component I; Provisional; Region: PRK13565 420662010605 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 420662010606 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 420662010607 SGNH_hydrolase, or GDSL_hydrolase, is 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 active site closely...; Region: SGNH_hydrolase; cd00229 420662010608 active site 420662010609 catalytic triad [active] 420662010610 oxyanion hole [active] 420662010611 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 420662010612 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 420662010613 substrate binding site [chemical binding]; other site 420662010614 hexamer interface [polypeptide binding]; other site 420662010615 metal binding site [ion binding]; metal-binding site 420662010616 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 420662010617 TPR motif; other site 420662010618 binding surface 420662010619 TPR repeat; Region: TPR_11; pfam13414 420662010620 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 420662010621 binding surface 420662010622 TPR motif; other site 420662010623 TPR repeat; Region: TPR_11; pfam13414 420662010624 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 420662010625 binding surface 420662010626 TPR motif; other site 420662010627 Tetratricopeptide repeat; Region: TPR_16; pfam13432 420662010628 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; pfam13759 420662010629 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 420662010630 Site-specific recombinase; Region: SpecificRecomb; pfam10136 420662010631 MltA specific insert domain; Region: MltA; smart00925 420662010632 3D domain; Region: 3D; pfam06725 420662010633 probable biosynthetic protein, Pnap_2097 family; Region: biosn_Pnap_2097; TIGR04099 420662010634 flavin-dependent oxidoreductase, MSMEG_0569 family; Region: MSMEG_0569_nitr; TIGR04046 420662010635 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662010636 MSMEG_0570 family protein; Region: MSMEG_0570_fam; TIGR04042 420662010637 glycosyltransferase, MSMEG_0565 family; Region: MSMEG_0565_glyc; TIGR04047 420662010638 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 420662010639 AIR synthase-related protein, sll0787 family; Region: AIR_rel_sll0787; TIGR04049 420662010640 AIR synthase (PurM) related protein, subgroup 3 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two...; Region: PurM-like3; cd02192 420662010641 dimerization interface [polypeptide binding]; other site 420662010642 putative ATP binding site [chemical binding]; other site 420662010643 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 420662010644 Coenzyme A binding pocket [chemical binding]; other site 420662010645 radical SAM protein, MSMEG_0568 family; Region: rSAM_MSMEG_0568; TIGR04043 420662010646 Predicted amidohydrolase [General function prediction only]; Region: COG0388 420662010647 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 420662010648 putative active site [active] 420662010649 catalytic triad [active] 420662010650 putative dimer interface [polypeptide binding]; other site 420662010651 MSMEG_0572 family protein; Region: MSMEG_0572_fam; TIGR04044 420662010652 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 420662010653 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662010654 DNA-binding site [nucleotide binding]; DNA binding site 420662010655 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 420662010656 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662010657 homodimer interface [polypeptide binding]; other site 420662010658 catalytic residue [active] 420662010659 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 420662010660 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 420662010661 active site residue [active] 420662010662 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 420662010663 SnoaL-like domain; Region: SnoaL_2; pfam12680 420662010664 cyanate hydratase; Validated; Region: PRK02866 420662010665 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 420662010666 oligomer interface [polypeptide binding]; other site 420662010667 active site 420662010668 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 420662010669 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 420662010670 Walker A/P-loop; other site 420662010671 ATP binding site [chemical binding]; other site 420662010672 Q-loop/lid; other site 420662010673 ABC transporter signature motif; other site 420662010674 Walker B; other site 420662010675 D-loop; other site 420662010676 H-loop/switch region; other site 420662010677 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 420662010678 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 420662010679 dimer interface [polypeptide binding]; other site 420662010680 conserved gate region; other site 420662010681 putative PBP binding loops; other site 420662010682 ABC-ATPase subunit interface; other site 420662010683 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 420662010684 NMT1-like family; Region: NMT1_2; pfam13379 420662010685 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662010686 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 420662010687 protein binding site [polypeptide binding]; other site 420662010688 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 420662010689 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 420662010690 Ligand Binding Site [chemical binding]; other site 420662010691 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 420662010692 Predicted membrane protein [Function unknown]; Region: COG3174 420662010693 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 420662010694 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 420662010695 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 420662010696 Beta-Casp domain; Region: Beta-Casp; smart01027 420662010697 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 420662010698 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662010699 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 420662010700 active site 420662010701 phosphorylation site [posttranslational modification] 420662010702 intermolecular recognition site; other site 420662010703 dimerization interface [polypeptide binding]; other site 420662010704 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 420662010705 DNA binding residues [nucleotide binding] 420662010706 dimerization interface [polypeptide binding]; other site 420662010707 PAS domain S-box; Region: sensory_box; TIGR00229 420662010708 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 420662010709 putative active site [active] 420662010710 heme pocket [chemical binding]; other site 420662010711 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 420662010712 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 420662010713 ATP binding site [chemical binding]; other site 420662010714 Mg2+ binding site [ion binding]; other site 420662010715 G-X-G motif; other site 420662010716 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662010717 GAF domain; Region: GAF; pfam01590 420662010718 PAS fold; Region: PAS_3; pfam08447 420662010719 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 420662010720 putative active site [active] 420662010721 heme pocket [chemical binding]; other site 420662010722 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662010723 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662010724 metal binding site [ion binding]; metal-binding site 420662010725 active site 420662010726 I-site; other site 420662010727 MOSC domain; Region: MOSC; pfam03473 420662010728 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 420662010729 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 420662010730 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662010731 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 420662010732 putative DNA binding site [nucleotide binding]; other site 420662010733 putative Zn2+ binding site [ion binding]; other site 420662010734 AsnC family; Region: AsnC_trans_reg; pfam01037 420662010735 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 420662010736 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 420662010737 dimer interface [polypeptide binding]; other site 420662010738 PYR/PP interface [polypeptide binding]; other site 420662010739 TPP binding site [chemical binding]; other site 420662010740 substrate binding site [chemical binding]; other site 420662010741 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 420662010742 TPP-binding site; other site 420662010743 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 420662010744 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; cl00447 420662010745 nudix motif; other site 420662010746 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 420662010747 dimerization interface [polypeptide binding]; other site 420662010748 substrate binding site [chemical binding]; other site 420662010749 active site 420662010750 calcium binding site [ion binding]; other site 420662010751 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 420662010752 YceI-like domain; Region: YceI; smart00867 420662010753 Uncharacterized conserved protein [Function unknown]; Region: COG2353 420662010754 Uncharacterized conserved protein [Function unknown]; Region: COG2353 420662010755 regulatory ATPase RavA; Provisional; Region: PRK13531 420662010756 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 420662010757 ATP binding site [chemical binding]; other site 420662010758 Walker A motif; other site 420662010759 Walker B motif; other site 420662010760 arginine finger; other site 420662010761 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 420662010762 metal ion-dependent adhesion site (MIDAS); other site 420662010763 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 420662010764 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 420662010765 PhoD-like phosphatase; Region: PhoD; pfam09423 420662010766 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 420662010767 putative active site [active] 420662010768 putative metal binding site [ion binding]; other site 420662010769 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 420662010770 transcriptional regulator, ArgP family; Region: argP; TIGR03298 420662010771 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662010772 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 420662010773 dimerization interface [polypeptide binding]; other site 420662010774 LysE type translocator; Region: LysE; cl00565 420662010775 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 420662010776 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662010777 hydroxyglutarate oxidase; Provisional; Region: PRK11728 420662010778 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 420662010779 VPS10 domain; Region: VPS10; smart00602 420662010780 Transcriptional regulator [Transcription]; Region: LysR; COG0583 420662010781 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662010782 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 420662010783 putative effector binding pocket; other site 420662010784 dimerization interface [polypeptide binding]; other site 420662010785 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 420662010786 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 420662010787 tetrameric interface [polypeptide binding]; other site 420662010788 NAD binding site [chemical binding]; other site 420662010789 catalytic residues [active] 420662010790 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 420662010791 short chain dehydrogenase; Provisional; Region: PRK06123 420662010792 classical (c) SDRs; Region: SDR_c; cd05233 420662010793 NAD(P) binding site [chemical binding]; other site 420662010794 active site 420662010795 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 420662010796 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 420662010797 Sporulation related domain; Region: SPOR; pfam05036 420662010798 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 420662010799 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 420662010800 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; pfam09982 420662010801 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 420662010802 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 420662010803 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 420662010804 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 420662010805 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 420662010806 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 420662010807 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 420662010808 DNA binding residues [nucleotide binding] 420662010809 dimer interface [polypeptide binding]; other site 420662010810 copper binding site [ion binding]; other site 420662010811 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 420662010812 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 420662010813 metal-binding site [ion binding] 420662010814 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 420662010815 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 420662010816 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 420662010817 metal-binding site [ion binding] 420662010818 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662010819 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 420662010820 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 420662010821 FAD binding domain; Region: FAD_binding_4; pfam01565 420662010822 Methyltransferase domain; Region: Methyltransf_11; pfam08241 420662010823 Protein of unknown function (DUF805); Region: DUF805; pfam05656 420662010824 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662010825 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 420662010826 putative C-terminal domain interface [polypeptide binding]; other site 420662010827 putative GSH binding site (G-site) [chemical binding]; other site 420662010828 putative dimer interface [polypeptide binding]; other site 420662010829 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 420662010830 N-terminal domain interface [polypeptide binding]; other site 420662010831 dimer interface [polypeptide binding]; other site 420662010832 substrate binding pocket (H-site) [chemical binding]; other site 420662010833 Cytochrome c; Region: Cytochrom_C; cl11414 420662010834 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 420662010835 putative hydrolase; Provisional; Region: PRK10985 420662010836 SnoaL-like domain; Region: SnoaL_3; pfam13474 420662010837 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 420662010838 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 420662010839 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 420662010840 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 420662010841 putative active site [active] 420662010842 putative substrate binding site [chemical binding]; other site 420662010843 putative cosubstrate binding site; other site 420662010844 catalytic site [active] 420662010845 RNA polymerase sigma factor; Provisional; Region: PRK12514 420662010846 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 420662010847 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 420662010848 DNA binding residues [nucleotide binding] 420662010849 Anti-sigma-K factor rskA; Region: RskA; pfam10099 420662010850 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 420662010851 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 420662010852 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 420662010853 putative active site [active] 420662010854 Zinc-finger domain; Region: zf-CHCC; cl01821 420662010855 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 420662010856 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 420662010857 homodimer interface [polypeptide binding]; other site 420662010858 substrate-cofactor binding pocket; other site 420662010859 catalytic residue [active] 420662010860 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 420662010861 DNA repair protein RadA; Provisional; Region: PRK11823 420662010862 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 420662010863 Walker A motif/ATP binding site; other site 420662010864 ATP binding site [chemical binding]; other site 420662010865 Walker B motif; other site 420662010866 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 420662010867 hypothetical protein; Provisional; Region: PRK09256 420662010868 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 420662010869 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 420662010870 Predicted membrane protein [Function unknown]; Region: COG2261 420662010871 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 420662010872 alanine racemase; Reviewed; Region: dadX; PRK03646 420662010873 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 420662010874 active site 420662010875 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 420662010876 substrate binding site [chemical binding]; other site 420662010877 catalytic residues [active] 420662010878 dimer interface [polypeptide binding]; other site 420662010879 lysophospholipid transporter LplT; Provisional; Region: PRK11195 420662010880 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 420662010881 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 420662010882 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 420662010883 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 420662010884 Ligand Binding Site [chemical binding]; other site 420662010885 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 420662010886 nudix motif; other site 420662010887 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 420662010888 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 420662010889 ligand binding site [chemical binding]; other site 420662010890 homodimer interface [polypeptide binding]; other site 420662010891 NAD(P) binding site [chemical binding]; other site 420662010892 trimer interface B [polypeptide binding]; other site 420662010893 trimer interface A [polypeptide binding]; other site 420662010894 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 420662010895 tetramerization interface [polypeptide binding]; other site 420662010896 active site 420662010897 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 420662010898 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 420662010899 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 420662010900 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 420662010901 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 420662010902 acyl-activating enzyme (AAE) consensus motif; other site 420662010903 putative AMP binding site [chemical binding]; other site 420662010904 putative active site [active] 420662010905 putative CoA binding site [chemical binding]; other site 420662010906 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 420662010907 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 420662010908 LrgA family; Region: LrgA; pfam03788 420662010909 hypothetical protein; Provisional; Region: PRK07907 420662010910 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 420662010911 metal binding site [ion binding]; metal-binding site 420662010912 putative dimer interface [polypeptide binding]; other site 420662010913 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 420662010914 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662010915 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662010916 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 420662010917 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 420662010918 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism]; Region: COG5424 420662010919 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 420662010920 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 420662010921 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 420662010922 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 420662010923 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 420662010924 active site 420662010925 phosphorylation site [posttranslational modification] 420662010926 intermolecular recognition site; other site 420662010927 dimerization interface [polypeptide binding]; other site 420662010928 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 420662010929 DNA binding residues [nucleotide binding] 420662010930 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 420662010931 Na binding site [ion binding]; other site 420662010932 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662010933 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 420662010934 dimer interface [polypeptide binding]; other site 420662010935 phosphorylation site [posttranslational modification] 420662010936 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 420662010937 ATP binding site [chemical binding]; other site 420662010938 Mg2+ binding site [ion binding]; other site 420662010939 G-X-G motif; other site 420662010940 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 420662010941 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 420662010942 active site 420662010943 phosphorylation site [posttranslational modification] 420662010944 intermolecular recognition site; other site 420662010945 dimerization interface [polypeptide binding]; other site 420662010946 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662010947 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 420662010948 putative ligand binding site [chemical binding]; other site 420662010949 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 420662010950 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662010951 TM-ABC transporter signature motif; other site 420662010952 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 420662010953 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 420662010954 TM-ABC transporter signature motif; other site 420662010955 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 420662010956 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662010957 Walker A/P-loop; other site 420662010958 ATP binding site [chemical binding]; other site 420662010959 Q-loop/lid; other site 420662010960 ABC transporter signature motif; other site 420662010961 Walker B; other site 420662010962 D-loop; other site 420662010963 H-loop/switch region; other site 420662010964 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 420662010965 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662010966 Walker A/P-loop; other site 420662010967 ATP binding site [chemical binding]; other site 420662010968 Q-loop/lid; other site 420662010969 ABC transporter signature motif; other site 420662010970 Walker B; other site 420662010971 D-loop; other site 420662010972 H-loop/switch region; other site 420662010973 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 420662010974 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 420662010975 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 420662010976 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 420662010977 putative substrate translocation pore; other site 420662010978 Fatty acid desaturase; Region: FA_desaturase; pfam00487 420662010979 The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of...; Region: Delta12-FADS-like; cd03507 420662010980 putative di-iron ligands [ion binding]; other site 420662010981 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 420662010982 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 420662010983 putative DNA binding site [nucleotide binding]; other site 420662010984 putative Zn2+ binding site [ion binding]; other site 420662010985 AsnC family; Region: AsnC_trans_reg; pfam01037 420662010986 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 420662010987 Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia; Region: ACCD; cd06449 420662010988 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662010989 catalytic residue [active] 420662010990 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 420662010991 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662010992 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 420662010993 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 420662010994 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 420662010995 Amidase; Region: Amidase; cl11426 420662010996 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 420662010997 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 420662010998 Phasin protein; Region: Phasin_2; pfam09361 420662010999 Glutamine cyclotransferase [Posttranslational modification, protein turnover, chaperones]; Region: COG3823 420662011000 Nuclease-related domain; Region: NERD; pfam08378 420662011001 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; cl17220 420662011002 dimerization interface [polypeptide binding]; other site 420662011003 putative DNA binding site [nucleotide binding]; other site 420662011004 putative Zn2+ binding site [ion binding]; other site 420662011005 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 420662011006 active site 420662011007 NTP binding site [chemical binding]; other site 420662011008 metal binding triad [ion binding]; metal-binding site 420662011009 antibiotic binding site [chemical binding]; other site 420662011010 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 420662011011 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 420662011012 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 420662011013 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 420662011014 multimer interface [polypeptide binding]; other site 420662011015 active site 420662011016 catalytic triad [active] 420662011017 dimer interface [polypeptide binding]; other site 420662011018 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 420662011019 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662011020 Walker A motif; other site 420662011021 ATP binding site [chemical binding]; other site 420662011022 Walker B motif; other site 420662011023 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 420662011024 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 420662011025 metal ion-dependent adhesion site (MIDAS); other site 420662011026 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 420662011027 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 420662011028 dimer interface [polypeptide binding]; other site 420662011029 active site 420662011030 metal binding site [ion binding]; metal-binding site 420662011031 glutathione binding site [chemical binding]; other site 420662011032 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 420662011033 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 420662011034 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 420662011035 active site 420662011036 FMN binding site [chemical binding]; other site 420662011037 substrate binding site [chemical binding]; other site 420662011038 3Fe-4S cluster binding site [ion binding]; other site 420662011039 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 420662011040 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 420662011041 active site 420662011042 phosphorylation site [posttranslational modification] 420662011043 intermolecular recognition site; other site 420662011044 dimerization interface [polypeptide binding]; other site 420662011045 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 420662011046 DNA binding residues [nucleotide binding] 420662011047 dimerization interface [polypeptide binding]; other site 420662011048 Histidine kinase; Region: HisKA_3; pfam07730 420662011049 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 420662011050 Mg2+ binding site [ion binding]; other site 420662011051 putative glutathione S-transferase; Provisional; Region: PRK10357 420662011052 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 420662011053 putative C-terminal domain interface [polypeptide binding]; other site 420662011054 putative GSH binding site (G-site) [chemical binding]; other site 420662011055 putative dimer interface [polypeptide binding]; other site 420662011056 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 420662011057 dimer interface [polypeptide binding]; other site 420662011058 N-terminal domain interface [polypeptide binding]; other site 420662011059 putative substrate binding pocket (H-site) [chemical binding]; other site 420662011060 adenylosuccinate lyase; Provisional; Region: PRK09285 420662011061 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 420662011062 tetramer interface [polypeptide binding]; other site 420662011063 active site 420662011064 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 420662011065 active site 420662011066 dimer interface [polypeptide binding]; other site 420662011067 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 420662011068 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 420662011069 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 420662011070 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 420662011071 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 420662011072 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 420662011073 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 420662011074 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 420662011075 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 420662011076 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 420662011077 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 420662011078 putative active site [active] 420662011079 putative dimer interface [polypeptide binding]; other site 420662011080 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 420662011081 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 420662011082 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 420662011083 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 420662011084 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 420662011085 Bacterial transcriptional regulator; Region: IclR; pfam01614 420662011086 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 420662011087 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 420662011088 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 420662011089 catalytic motif [active] 420662011090 Catalytic residue [active] 420662011091 FIST N domain; Region: FIST; smart00897 420662011092 FIST C domain; Region: FIST_C; pfam10442 420662011093 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 420662011094 FAD binding domain; Region: FAD_binding_4; pfam01565 420662011095 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 420662011096 FAD binding domain; Region: FAD_binding_4; pfam01565 420662011097 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 420662011098 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 420662011099 Cysteine-rich domain; Region: CCG; pfam02754 420662011100 Cysteine-rich domain; Region: CCG; pfam02754 420662011101 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 420662011102 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 420662011103 EamA-like transporter family; Region: EamA; pfam00892 420662011104 EamA-like transporter family; Region: EamA; pfam00892 420662011105 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 420662011106 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 420662011107 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662011108 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 420662011109 active site residue [active] 420662011110 Uncharacterized conserved protein [Function unknown]; Region: COG1739 420662011111 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 420662011112 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 420662011113 recombination associated protein; Reviewed; Region: rdgC; PRK00321 420662011114 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 420662011115 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 420662011116 tetramer interface [polypeptide binding]; other site 420662011117 active site 420662011118 Mg2+/Mn2+ binding site [ion binding]; other site 420662011119 Dehydratase family; Region: ILVD_EDD; pfam00920 420662011120 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 420662011121 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 420662011122 DctM-like transporters; Region: DctM; pfam06808 420662011123 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 420662011124 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 420662011125 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662011126 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 420662011127 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate; Region: HHD; cd08191 420662011128 putative active site [active] 420662011129 metal binding site [ion binding]; metal-binding site 420662011130 Transcriptional regulators [Transcription]; Region: GntR; COG1802 420662011131 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662011132 DNA-binding site [nucleotide binding]; DNA binding site 420662011133 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 420662011134 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 420662011135 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 420662011136 Trp docking motif [polypeptide binding]; other site 420662011137 active site 420662011138 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 420662011139 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 420662011140 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 420662011141 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662011142 CsbD-like; Region: CsbD; cl17424 420662011143 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 420662011144 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662011145 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 420662011146 glycerol kinase; Provisional; Region: glpK; PRK00047 420662011147 N- and C-terminal domain interface [polypeptide binding]; other site 420662011148 active site 420662011149 MgATP binding site [chemical binding]; other site 420662011150 catalytic site [active] 420662011151 metal binding site [ion binding]; metal-binding site 420662011152 glycerol binding site [chemical binding]; other site 420662011153 homotetramer interface [polypeptide binding]; other site 420662011154 homodimer interface [polypeptide binding]; other site 420662011155 FBP binding site [chemical binding]; other site 420662011156 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 420662011157 active site 420662011158 Putative cyclase; Region: Cyclase; pfam04199 420662011159 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 420662011160 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662011161 Transcriptional regulator [Transcription]; Region: IclR; COG1414 420662011162 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 420662011163 putative DNA binding site [nucleotide binding]; other site 420662011164 putative Zn2+ binding site [ion binding]; other site 420662011165 Bacterial transcriptional regulator; Region: IclR; pfam01614 420662011166 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662011167 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 420662011168 iron-sulfur cluster [ion binding]; other site 420662011169 [2Fe-2S] cluster binding site [ion binding]; other site 420662011170 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662011171 hydrophobic ligand binding site; other site 420662011172 Rubredoxin [Energy production and conversion]; Region: COG1773 420662011173 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 420662011174 iron binding site [ion binding]; other site 420662011175 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662011176 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 420662011177 putative ligand binding site [chemical binding]; other site 420662011178 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 420662011179 TM-ABC transporter signature motif; other site 420662011180 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 420662011181 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662011182 TM-ABC transporter signature motif; other site 420662011183 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 420662011184 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662011185 Walker A/P-loop; other site 420662011186 ATP binding site [chemical binding]; other site 420662011187 Q-loop/lid; other site 420662011188 ABC transporter signature motif; other site 420662011189 Walker B; other site 420662011190 D-loop; other site 420662011191 H-loop/switch region; other site 420662011192 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 420662011193 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662011194 Walker A/P-loop; other site 420662011195 ATP binding site [chemical binding]; other site 420662011196 Q-loop/lid; other site 420662011197 ABC transporter signature motif; other site 420662011198 Walker B; other site 420662011199 D-loop; other site 420662011200 H-loop/switch region; other site 420662011201 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 420662011202 CoA-transferase family III; Region: CoA_transf_3; pfam02515 420662011203 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 420662011204 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 420662011205 substrate binding site [chemical binding]; other site 420662011206 oxyanion hole (OAH) forming residues; other site 420662011207 trimer interface [polypeptide binding]; other site 420662011208 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 420662011209 EamA-like transporter family; Region: EamA; pfam00892 420662011210 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 420662011211 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 420662011212 C-terminal domain interface [polypeptide binding]; other site 420662011213 GSH binding site (G-site) [chemical binding]; other site 420662011214 dimer interface [polypeptide binding]; other site 420662011215 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 420662011216 N-terminal domain interface [polypeptide binding]; other site 420662011217 dimer interface [polypeptide binding]; other site 420662011218 substrate binding pocket (H-site) [chemical binding]; other site 420662011219 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 420662011220 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 420662011221 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 420662011222 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662011223 homodimer interface [polypeptide binding]; other site 420662011224 catalytic residue [active] 420662011225 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 420662011226 catalytic residues [active] 420662011227 dimer interface [polypeptide binding]; other site 420662011228 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 420662011229 Response regulator receiver domain; Region: Response_reg; pfam00072 420662011230 active site 420662011231 phosphorylation site [posttranslational modification] 420662011232 intermolecular recognition site; other site 420662011233 dimerization interface [polypeptide binding]; other site 420662011234 NMT1/THI5 like; Region: NMT1; pfam09084 420662011235 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 420662011236 HDOD domain; Region: HDOD; pfam08668 420662011237 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 420662011238 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 420662011239 FMN binding site [chemical binding]; other site 420662011240 active site 420662011241 substrate binding site [chemical binding]; other site 420662011242 catalytic residue [active] 420662011243 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 420662011244 GAF domain; Region: GAF_2; pfam13185 420662011245 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 420662011246 PAS domain; Region: PAS_9; pfam13426 420662011247 putative active site [active] 420662011248 heme pocket [chemical binding]; other site 420662011249 PAS domain; Region: PAS_9; pfam13426 420662011250 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 420662011251 dimer interface [polypeptide binding]; other site 420662011252 phosphorylation site [posttranslational modification] 420662011253 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 420662011254 ATP binding site [chemical binding]; other site 420662011255 Mg2+ binding site [ion binding]; other site 420662011256 G-X-G motif; other site 420662011257 Response regulator receiver domain; Region: Response_reg; pfam00072 420662011258 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 420662011259 active site 420662011260 phosphorylation site [posttranslational modification] 420662011261 intermolecular recognition site; other site 420662011262 dimerization interface [polypeptide binding]; other site 420662011263 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 420662011264 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662011265 Walker A/P-loop; other site 420662011266 ATP binding site [chemical binding]; other site 420662011267 Q-loop/lid; other site 420662011268 ABC transporter signature motif; other site 420662011269 Walker B; other site 420662011270 D-loop; other site 420662011271 H-loop/switch region; other site 420662011272 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 420662011273 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662011274 Walker A/P-loop; other site 420662011275 ATP binding site [chemical binding]; other site 420662011276 Q-loop/lid; other site 420662011277 ABC transporter signature motif; other site 420662011278 Walker B; other site 420662011279 D-loop; other site 420662011280 H-loop/switch region; other site 420662011281 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 420662011282 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 420662011283 dimer interface [polypeptide binding]; other site 420662011284 conserved gate region; other site 420662011285 putative PBP binding loops; other site 420662011286 ABC-ATPase subunit interface; other site 420662011287 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 420662011288 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 420662011289 dimer interface [polypeptide binding]; other site 420662011290 conserved gate region; other site 420662011291 putative PBP binding loops; other site 420662011292 ABC-ATPase subunit interface; other site 420662011293 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 420662011294 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_18; cd08505 420662011295 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 420662011296 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 420662011297 putative active site [active] 420662011298 putative catalytic site [active] 420662011299 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 420662011300 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 420662011301 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 420662011302 Ligand Binding Site [chemical binding]; other site 420662011303 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 420662011304 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 420662011305 active site 420662011306 metal binding site [ion binding]; metal-binding site 420662011307 hypothetical protein; Provisional; Region: PRK10396 420662011308 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 420662011309 SEC-C motif; Region: SEC-C; pfam02810 420662011310 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_GTP; cd00819 420662011311 active site 420662011312 substrate-binding site [chemical binding]; other site 420662011313 metal-binding site [ion binding] 420662011314 GTP binding site [chemical binding]; other site 420662011315 PBP superfamily domain; Region: PBP_like_2; pfam12849 420662011316 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 420662011317 PBP superfamily domain; Region: PBP_like; pfam12727 420662011318 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 420662011319 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a...; Region: TRX_Fd_NuoE_FDH_gamma; cd03081 420662011320 putative dimer interface [polypeptide binding]; other site 420662011321 [2Fe-2S] cluster binding site [ion binding]; other site 420662011322 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 420662011323 putative dimer interface [polypeptide binding]; other site 420662011324 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 420662011325 SLBB domain; Region: SLBB; pfam10531 420662011326 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 420662011327 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 420662011328 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 420662011329 catalytic loop [active] 420662011330 iron binding site [ion binding]; other site 420662011331 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 420662011332 4Fe-4S binding domain; Region: Fer4; pfam00037 420662011333 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 420662011334 [4Fe-4S] binding site [ion binding]; other site 420662011335 molybdopterin cofactor binding site; other site 420662011336 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 420662011337 molybdopterin cofactor binding site; other site 420662011338 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 420662011339 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 420662011340 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 420662011341 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 420662011342 conserved gate region; other site 420662011343 putative PBP binding loops; other site 420662011344 ABC-ATPase subunit interface; other site 420662011345 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 420662011346 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662011347 Walker A/P-loop; other site 420662011348 ATP binding site [chemical binding]; other site 420662011349 Q-loop/lid; other site 420662011350 ABC transporter signature motif; other site 420662011351 Walker B; other site 420662011352 D-loop; other site 420662011353 H-loop/switch region; other site 420662011354 TOBE domain; Region: TOBE; cl01440 420662011355 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 420662011356 MOSC domain; Region: MOSC; pfam03473 420662011357 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 420662011358 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 420662011359 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 420662011360 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 420662011361 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 420662011362 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 420662011363 TolR protein; Region: tolR; TIGR02801 420662011364 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 420662011365 HlyD family secretion protein; Region: HlyD_3; pfam13437 420662011366 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 420662011367 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 420662011368 Walker A/P-loop; other site 420662011369 ATP binding site [chemical binding]; other site 420662011370 Q-loop/lid; other site 420662011371 ABC transporter signature motif; other site 420662011372 Walker B; other site 420662011373 D-loop; other site 420662011374 H-loop/switch region; other site 420662011375 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 420662011376 FtsX-like permease family; Region: FtsX; pfam02687 420662011377 Outer membrane efflux protein; Region: OEP; pfam02321 420662011378 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 420662011379 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 420662011380 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 420662011381 N-terminal plug; other site 420662011382 ligand-binding site [chemical binding]; other site 420662011383 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 420662011384 Flavodoxin; Region: Flavodoxin_1; pfam00258 420662011385 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 420662011386 FAD binding pocket [chemical binding]; other site 420662011387 FAD binding motif [chemical binding]; other site 420662011388 catalytic residues [active] 420662011389 NAD binding pocket [chemical binding]; other site 420662011390 phosphate binding motif [ion binding]; other site 420662011391 beta-alpha-beta structure motif; other site 420662011392 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 420662011393 ApbE family; Region: ApbE; pfam02424 420662011394 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 420662011395 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 420662011396 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 420662011397 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 420662011398 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 420662011399 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 420662011400 N-terminal plug; other site 420662011401 ligand-binding site [chemical binding]; other site 420662011402 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 420662011403 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 420662011404 putative acyl-acceptor binding pocket; other site 420662011405 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 420662011406 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 420662011407 Ion channel; Region: Ion_trans_2; pfam07885 420662011408 Cytochrome c; Region: Cytochrom_C; cl11414 420662011409 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 420662011410 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 420662011411 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 420662011412 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 420662011413 generic binding surface II; other site 420662011414 ssDNA binding site; other site 420662011415 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 420662011416 ATP binding site [chemical binding]; other site 420662011417 putative Mg++ binding site [ion binding]; other site 420662011418 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 420662011419 nucleotide binding region [chemical binding]; other site 420662011420 ATP-binding site [chemical binding]; other site 420662011421 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 420662011422 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 420662011423 substrate binding pocket [chemical binding]; other site 420662011424 membrane-bound complex binding site; other site 420662011425 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 420662011426 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 420662011427 substrate binding pocket [chemical binding]; other site 420662011428 membrane-bound complex binding site; other site 420662011429 hinge residues; other site 420662011430 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662011431 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 420662011432 ATP binding site [chemical binding]; other site 420662011433 Mg2+ binding site [ion binding]; other site 420662011434 G-X-G motif; other site 420662011435 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 420662011436 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 420662011437 active site 420662011438 phosphorylation site [posttranslational modification] 420662011439 intermolecular recognition site; other site 420662011440 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 420662011441 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 420662011442 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 420662011443 dimerization interface [polypeptide binding]; other site 420662011444 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 420662011445 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 420662011446 dimer interface [polypeptide binding]; other site 420662011447 active site 420662011448 heme binding site [chemical binding]; other site 420662011449 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 420662011450 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 420662011451 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 420662011452 dimerization interface [polypeptide binding]; other site 420662011453 DPS ferroxidase diiron center [ion binding]; other site 420662011454 ion pore; other site 420662011455 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 420662011456 PLD-like domain; Region: PLDc_2; pfam13091 420662011457 putative active site [active] 420662011458 catalytic site [active] 420662011459 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 420662011460 PLD-like domain; Region: PLDc_2; pfam13091 420662011461 putative active site [active] 420662011462 catalytic site [active] 420662011463 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 420662011464 UbiA prenyltransferase family; Region: UbiA; pfam01040 420662011465 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 420662011466 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 420662011467 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 420662011468 NAD(P) binding site [chemical binding]; other site 420662011469 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 420662011470 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 420662011471 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 420662011472 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 420662011473 Glutamate binding site [chemical binding]; other site 420662011474 NAD binding site [chemical binding]; other site 420662011475 catalytic residues [active] 420662011476 Proline dehydrogenase; Region: Pro_dh; cl03282 420662011477 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 420662011478 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 420662011479 putative DNA binding site [nucleotide binding]; other site 420662011480 putative Zn2+ binding site [ion binding]; other site 420662011481 AsnC family; Region: AsnC_trans_reg; pfam01037 420662011482 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 420662011483 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 420662011484 Uncharacterized protein conserved in bacteria (DUF2086); Region: DUF2086; pfam09859 420662011485 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 420662011486 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 420662011487 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662011488 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 420662011489 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 420662011490 DNA binding site [nucleotide binding] 420662011491 active site 420662011492 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 420662011493 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662011494 Walker A/P-loop; other site 420662011495 ATP binding site [chemical binding]; other site 420662011496 Q-loop/lid; other site 420662011497 ABC transporter signature motif; other site 420662011498 Walker B; other site 420662011499 D-loop; other site 420662011500 H-loop/switch region; other site 420662011501 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 420662011502 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662011503 Walker A/P-loop; other site 420662011504 ATP binding site [chemical binding]; other site 420662011505 Q-loop/lid; other site 420662011506 ABC transporter signature motif; other site 420662011507 Walker B; other site 420662011508 D-loop; other site 420662011509 H-loop/switch region; other site 420662011510 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662011511 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 420662011512 putative ligand binding site [chemical binding]; other site 420662011513 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 420662011514 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662011515 TM-ABC transporter signature motif; other site 420662011516 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 420662011517 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 420662011518 TM-ABC transporter signature motif; other site 420662011519 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 420662011520 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 420662011521 catalytic residue [active] 420662011522 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 420662011523 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 420662011524 Walker A motif; other site 420662011525 ATP binding site [chemical binding]; other site 420662011526 Walker B motif; other site 420662011527 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662011528 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 420662011529 ligand binding site [chemical binding]; other site 420662011530 flexible hinge region; other site 420662011531 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 420662011532 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 420662011533 Walker A motif; other site 420662011534 ATP binding site [chemical binding]; other site 420662011535 Walker B motif; other site 420662011536 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 420662011537 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 420662011538 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 420662011539 BON domain; Region: BON; pfam04972 420662011540 BON domain; Region: BON; pfam04972 420662011541 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 420662011542 dimer interface [polypeptide binding]; other site 420662011543 active site 420662011544 hypothetical protein; Provisional; Region: PRK14673 420662011545 Predicted methyltransferases [General function prediction only]; Region: COG0313 420662011546 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 420662011547 putative SAM binding site [chemical binding]; other site 420662011548 putative homodimer interface [polypeptide binding]; other site 420662011549 protease TldD; Provisional; Region: tldD; PRK10735 420662011550 threonine dehydratase; Provisional; Region: PRK07334 420662011551 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 420662011552 tetramer interface [polypeptide binding]; other site 420662011553 pyridoxal 5'-phosphate binding site [chemical binding]; other site 420662011554 catalytic residue [active] 420662011555 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 420662011556 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 420662011557 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 420662011558 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 420662011559 EF-hand domain pair; Region: EF_hand_5; pfam13499 420662011560 pseudo EF-hand loop; other site 420662011561 peptide binding pocket; other site 420662011562 Ca2+ binding site [ion binding]; other site 420662011563 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 420662011564 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 420662011565 FAD binding domain; Region: FAD_binding_4; pfam01565 420662011566 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 420662011567 GAF domain; Region: GAF; pfam01590 420662011568 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 420662011569 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 420662011570 metal binding site [ion binding]; metal-binding site 420662011571 active site 420662011572 I-site; other site 420662011573 SpoVR family protein; Provisional; Region: PRK11767 420662011574 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 420662011575 hypothetical protein; Provisional; Region: PRK05325 420662011576 PrkA family serine protein kinase; Provisional; Region: PRK15455 420662011577 AAA ATPase domain; Region: AAA_16; pfam13191 420662011578 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 420662011579 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 420662011580 ParB-like nuclease domain; Region: ParB; smart00470 420662011581 Serine hydrolase; Region: Ser_hydrolase; pfam06821 420662011582 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 420662011583 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 420662011584 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 420662011585 P-loop; other site 420662011586 Magnesium ion binding site [ion binding]; other site 420662011587 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 420662011588 Magnesium ion binding site [ion binding]; other site 420662011589 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 420662011590 homotetrameric interface [polypeptide binding]; other site 420662011591 putative active site [active] 420662011592 metal binding site [ion binding]; metal-binding site 420662011593 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 420662011594 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 420662011595 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 420662011596 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 420662011597 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 420662011598 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 420662011599 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 420662011600 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 420662011601 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 420662011602 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 420662011603 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 420662011604 active site 420662011605 homotetramer interface [polypeptide binding]; other site 420662011606 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 420662011607 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 420662011608 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 420662011609 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 420662011610 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 420662011611 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 420662011612 putative active site [active] 420662011613 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 420662011614 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 420662011615 Walker A/P-loop; other site 420662011616 ATP binding site [chemical binding]; other site 420662011617 Q-loop/lid; other site 420662011618 ABC transporter signature motif; other site 420662011619 Walker B; other site 420662011620 D-loop; other site 420662011621 H-loop/switch region; other site 420662011622 NHLM bacteriocin system secretion protein; Region: NHLM_micro_HlyD; TIGR03794 420662011623 Autoinducer binding domain; Region: Autoind_bind; pfam03472 420662011624 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 420662011625 DNA binding residues [nucleotide binding] 420662011626 dimerization interface [polypeptide binding]; other site 420662011627 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 420662011628 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 420662011629 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 420662011630 ATP-binding cassette domain of the Na+ transporter; Region: ABC_NatA_sodium_exporter; cd03266 420662011631 Walker A/P-loop; other site 420662011632 ATP binding site [chemical binding]; other site 420662011633 Q-loop/lid; other site 420662011634 ABC transporter signature motif; other site 420662011635 Walker B; other site 420662011636 D-loop; other site 420662011637 H-loop/switch region; other site 420662011638 TAP-like protein; Region: Abhydrolase_4; pfam08386 420662011639 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 420662011640 hypothetical protein; Provisional; Region: PRK10621 420662011641 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 420662011642 choline dehydrogenase; Validated; Region: PRK02106 420662011643 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 420662011644 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 420662011645 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 420662011646 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 420662011647 short chain dehydrogenase; Provisional; Region: PRK07024 420662011648 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 420662011649 NAD(P) binding site [chemical binding]; other site 420662011650 active site 420662011651 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 420662011652 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 420662011653 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 420662011654 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 420662011655 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 420662011656 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 420662011657 putative active site [active] 420662011658 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 420662011659 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 420662011660 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 420662011661 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 420662011662 TrkA-N domain; Region: TrkA_N; pfam02254 420662011663 TrkA-C domain; Region: TrkA_C; pfam02080 420662011664 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 420662011665 catalytic core [active] 420662011666 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 420662011667 active site 420662011668 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 420662011669 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 420662011670 ligand binding site [chemical binding]; other site 420662011671 flexible hinge region; other site 420662011672 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 420662011673 active site 420662011674 Int/Topo IB signature motif; other site 420662011675 DNA binding site [nucleotide binding] 420662011676 Helix-turn-helix domain; Region: HTH_17; pfam12728 420662011677 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 420662011678 Transposase domain (DUF772); Region: DUF772; pfam05598 420662011679 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 420662011680 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662011681 US22 family homolog; Provisional; Region: PHA03344 420662011682 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 420662011683 DNA methylase; Region: N6_N4_Mtase; pfam01555 420662011684 integrase; Provisional; Region: PRK09692 420662011685 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 420662011686 active site 420662011687 Int/Topo IB signature motif; other site 420662011688 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 420662011689 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 420662011690 trmE is a tRNA modification GTPase; Region: trmE; cd04164 420662011691 G1 box; other site 420662011692 GTP/Mg2+ binding site [chemical binding]; other site 420662011693 Switch I region; other site 420662011694 G2 box; other site 420662011695 Switch II region; other site 420662011696 G3 box; other site 420662011697 G4 box; other site 420662011698 G5 box; other site 420662011699 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 420662011700 membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Region: yidC_nterm; TIGR03593 420662011701 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 420662011702 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 420662011703 Haemolytic domain; Region: Haemolytic; cl00506 420662011704 Ribonuclease P; Region: Ribonuclease_P; pfam00825 420662011705 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 420662011706 putative transposase OrfB; Reviewed; Region: PHA02517 420662011707 HTH-like domain; Region: HTH_21; pfam13276 420662011708 Integrase core domain; Region: rve; pfam00665 420662011709 Integrase core domain; Region: rve_3; pfam13683 420662011710 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662011711 Transposase; Region: HTH_Tnp_1; pfam01527 420662011712 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 420662011713 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 420662011714 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 420662011715 active site 420662011716 DNA binding site [nucleotide binding] 420662011717 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 420662011718 DNA binding site [nucleotide binding] 420662011719 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 420662011720 nucleotide binding site [chemical binding]; other site 420662011721 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 420662011722 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 420662011723 active site 420662011724 Zn binding site [ion binding]; other site 420662011725 PilZ domain; Region: PilZ; pfam07238 420662011726 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; cl02529 420662011727 SIR2 superfamily 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; cd00296 420662011728 stage V sporulation protein K; Region: spore_V_K; TIGR02881 420662011729 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 420662011730 Walker A motif; other site 420662011731 ATP binding site [chemical binding]; other site 420662011732 Walker B motif; other site 420662011733 arginine finger; other site 420662011734 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 420662011735 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 420662011736 active site 420662011737 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 420662011738 HNH endonuclease; Region: HNH_2; pfam13391 420662011739 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 420662011740 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 420662011741 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 420662011742 Catalytic site [active] 420662011743 Protein of unknown function (DUF4236); Region: DUF4236; pfam14020 420662011744 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 420662011745 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 420662011746 active site 420662011747 DNA binding site [nucleotide binding] 420662011748 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 420662011749 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 420662011750 Peptidase M15; Region: Peptidase_M15_3; cl01194 420662011751 AAA-like domain; Region: AAA_10; pfam12846 420662011752 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 420662011753 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 420662011754 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662011755 catalytic residue [active] 420662011756 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 420662011757 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 420662011758 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 420662011759 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 420662011760 ParB-like nuclease domain; Region: ParB; smart00470 420662011761 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 420662011762 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 420662011763 putative transposase OrfB; Reviewed; Region: PHA02517 420662011764 HTH-like domain; Region: HTH_21; pfam13276 420662011765 Integrase core domain; Region: rve; pfam00665 420662011766 Integrase core domain; Region: rve_3; pfam13683 420662011767 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662011768 Transposase; Region: HTH_Tnp_1; pfam01527 420662011769 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 420662011770 dimer interface [polypeptide binding]; other site 420662011771 phosphorylation site [posttranslational modification] 420662011772 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 420662011773 ATP binding site [chemical binding]; other site 420662011774 Mg2+ binding site [ion binding]; other site 420662011775 G-X-G motif; other site 420662011776 Response regulator receiver domain; Region: Response_reg; pfam00072 420662011777 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 420662011778 active site 420662011779 phosphorylation site [posttranslational modification] 420662011780 intermolecular recognition site; other site 420662011781 dimerization interface [polypeptide binding]; other site 420662011782 Phage integrase protein; Region: DUF3701; pfam12482 420662011783 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 420662011784 active site 420662011785 DNA binding site [nucleotide binding] 420662011786 Int/Topo IB signature motif; other site 420662011787 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 420662011788 ParB-like nuclease domain; Region: ParB; smart00470 420662011789 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 420662011790 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 420662011791 P-loop; other site 420662011792 Magnesium ion binding site [ion binding]; other site 420662011793 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 420662011794 Magnesium ion binding site [ion binding]; other site 420662011795 Initiator Replication protein; Region: Rep_3; pfam01051 420662011796 Protein of unknown function (DUF736); Region: DUF736; cl02303 420662011797 Initiator Replication protein; Region: Rep_3; pfam01051 420662011798 Whirly transcription factor; Region: Whirly; pfam08536 420662011799 HDOD domain; Region: HDOD; pfam08668 420662011800 Methyltransferase domain; Region: Methyltransf_26; pfam13659 420662011801 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 420662011802 Predicted helicase [General function prediction only]; Region: COG4889 420662011803 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 420662011804 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 420662011805 ATP binding site [chemical binding]; other site 420662011806 putative Mg++ binding site [ion binding]; other site 420662011807 nucleotide binding region [chemical binding]; other site 420662011808 Helicase conserved C-terminal domain; Region: Helicase_C; pfam00271 420662011809 ATP-binding site [chemical binding]; other site 420662011810 Methyltransferase domain; Region: Methyltransf_26; pfam13659 420662011811 Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs; Region: Piwi_piwi-like_ProArk; cd04659 420662011812 5' RNA guide strand anchoring site; other site 420662011813 active site 420662011814 Protein of unknown function (DUF3563); Region: DUF3563; pfam12086 420662011815 RDD family; Region: RDD; pfam06271 420662011816 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 420662011817 Mg binding site [ion binding]; other site 420662011818 nucleotide binding site [chemical binding]; other site 420662011819 putative protofilament interface [polypeptide binding]; other site 420662011820 AAA domain; Region: AAA_30; pfam13604 420662011821 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 420662011822 Family description; Region: UvrD_C_2; pfam13538 420662011823 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 420662011824 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 420662011825 putative active site [active] 420662011826 metal binding site [ion binding]; metal-binding site 420662011827 RNA polymerase recycling family C-terminal; Region: RapA_C; pfam12137 420662011828 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl17483 420662011829 HAMP domain; Region: HAMP; pfam00672 420662011830 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 420662011831 dimer interface [polypeptide binding]; other site 420662011832 putative CheW interface [polypeptide binding]; other site 420662011833 cystathionine beta-lyase; Provisional; Region: PRK07050 420662011834 thymidylate synthase; Provisional; Region: thyA; PRK13821 420662011835 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 420662011836 dimerization interface [polypeptide binding]; other site 420662011837 active site 420662011838 Staphylococcal nuclease homologues; Region: SNc; smart00318 420662011839 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 420662011840 Catalytic site; other site 420662011841 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 420662011842 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 420662011843 RNA/DNA hybrid binding site [nucleotide binding]; other site 420662011844 active site 420662011845 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 420662011846 deoxycytidine triphosphate deaminase; Reviewed; Region: dcd; PRK00416 420662011847 Protein of unknown function (DUF4007); Region: DUF4007; pfam13182 420662011848 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 420662011849 Active Sites [active] 420662011850 Protein of unknown function DUF262; Region: DUF262; pfam03235 420662011851 Uncharacterized conserved protein [Function unknown]; Region: COG1479 420662011852 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 420662011853 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 420662011854 Methyltransferase domain; Region: Methyltransf_23; pfam13489 420662011855 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 420662011856 S-adenosylmethionine binding site [chemical binding]; other site 420662011857 DNA phosphorothioation-associated putative methyltransferase; Region: dnd_rel_methyl; TIGR04096 420662011858 Peptidase M15; Region: Peptidase_M15_3; cl01194 420662011859 putative transposase OrfB; Reviewed; Region: PHA02517 420662011860 HTH-like domain; Region: HTH_21; pfam13276 420662011861 Integrase core domain; Region: rve; pfam00665 420662011862 Integrase core domain; Region: rve_3; pfam13683 420662011863 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662011864 Transposase; Region: HTH_Tnp_1; pfam01527 420662011865 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 420662011866 ParB-like nuclease domain; Region: ParB; smart00470 420662011867 RepB plasmid partitioning protein; Region: RepB; pfam07506 420662011868 ParB-like nuclease domain; Region: ParB; smart00470 420662011869 RepB plasmid partitioning protein; Region: RepB; pfam07506 420662011870 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 420662011871 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 420662011872 catalytic residues [active] 420662011873 catalytic nucleophile [active] 420662011874 Recombinase; Region: Recombinase; pfam07508 420662011875 HNH endonuclease; Region: HNH_2; pfam13391 420662011876 DnaB-like helicase C terminal domain; Region: DnaB_C; pfam03796 420662011877 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 420662011878 Walker A motif; other site 420662011879 ATP binding site [chemical binding]; other site 420662011880 Walker B motif; other site 420662011881 DNA binding loops [nucleotide binding] 420662011882 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 420662011883 non-specific DNA binding site [nucleotide binding]; other site 420662011884 salt bridge; other site 420662011885 sequence-specific DNA binding site [nucleotide binding]; other site 420662011886 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 420662011887 catalytic motif [active] 420662011888 Zn binding site [ion binding]; other site 420662011889 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 420662011890 active site 420662011891 Int/Topo IB signature motif; other site 420662011892 DNA binding site [nucleotide binding] 420662011893 Domain of Unknown Function with PDB structure (DUF3850); Region: DUF3850; pfam12961 420662011894 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662011895 Transposase; Region: HTH_Tnp_1; cl17663 420662011896 Restriction alleviation protein Lar; Region: Lar_restr_allev; cl08047 420662011897 Transposase; Region: HTH_Tnp_1; cl17663 420662011898 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662011899 CTP synthetase; Validated; Region: pyrG; PRK05380 420662011900 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 420662011901 active site 420662011902 UTP binding site [chemical binding]; other site 420662011903 Catalytic site [active] 420662011904 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 420662011905 active site 420662011906 putative oxyanion hole; other site 420662011907 catalytic triad [active] 420662011908 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 420662011909 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 420662011910 folate binding site [chemical binding]; other site 420662011911 NADP+ binding site [chemical binding]; other site 420662011912 Methyltransferase domain; Region: Methyltransf_26; pfam13659 420662011913 Arv1-like family; Region: Arv1; pfam04161 420662011914 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 420662011915 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 420662011916 catalytic residues [active] 420662011917 5'-3' exonuclease; Region: 53EXOc; smart00475 420662011918 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 420662011919 active site 420662011920 metal binding site 1 [ion binding]; metal-binding site 420662011921 putative 5' ssDNA interaction site; other site 420662011922 metal binding site 3; metal-binding site 420662011923 metal binding site 2 [ion binding]; metal-binding site 420662011924 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 420662011925 putative DNA binding site [nucleotide binding]; other site 420662011926 putative metal binding site [ion binding]; other site 420662011927 thymidylate kinase; Validated; Region: tmk; PRK00698 420662011928 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 420662011929 TMP-binding site; other site 420662011930 ATP-binding site [chemical binding]; other site 420662011931 recombination associated protein; Reviewed; Region: rdgC; PRK00321 420662011932 enoyl-CoA hydratase; Validated; Region: PRK08788 420662011933 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 420662011934 substrate binding site [chemical binding]; other site 420662011935 oxyanion hole (OAH) forming residues; other site 420662011936 trimer interface [polypeptide binding]; other site 420662011937 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662011938 dinuclear metal binding motif [ion binding]; other site 420662011939 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 420662011940 ligand binding site [chemical binding]; other site 420662011941 active site 420662011942 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 420662011943 active site 420662011944 hypothetical protein; Region: PHA00684 420662011945 DNA ligase; Provisional; Region: 30; PHA02587 420662011946 Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; Region: Adenylation_DNA_ligase_like; cd06846 420662011947 active site 420662011948 The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; Region: OBF_DNA_ligase_family; cl08424 420662011949 DNA binding site [nucleotide binding] 420662011950 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 420662011951 active site 420662011952 metal binding site [ion binding]; metal-binding site 420662011953 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 420662011954 ATP binding site [chemical binding]; other site 420662011955 putative Mg++ binding site [ion binding]; other site 420662011956 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 420662011957 nucleotide binding region [chemical binding]; other site 420662011958 ATP-binding site [chemical binding]; other site 420662011959 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 bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 420662011960 putative active site [active] 420662011961 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 420662011962 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 420662011963 Walker A motif; other site 420662011964 ATP binding site [chemical binding]; other site 420662011965 Walker B motif; other site 420662011966 arginine finger; other site 420662011967 Mrr N-terminal domain; Region: Mrr_N; pfam14338 420662011968 DNA methylase; Region: N6_N4_Mtase; pfam01555 420662011969 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 420662011970 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 420662011971 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 420662011972 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 420662011973 S-adenosylmethionine binding site [chemical binding]; other site 420662011974 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; cl00075 420662011975 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 420662011976 trimer interface [polypeptide binding]; other site 420662011977 active site 420662011978 Domain of unknown function (DUF4326); Region: DUF4326; pfam14216 420662011979 Domain of unknown function (DUF1768); Region: DUF1768; pfam08719 420662011980 Protein of unknown function (DUF1064); Region: DUF1064; pfam06356 420662011981 HD domain; Region: HD_4; pfam13328 420662011982 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; cl17321 420662011983 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 420662011984 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 420662011985 active site 420662011986 ERCC4 domain; Region: ERCC4; pfam02732 420662011987 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 420662011988 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 420662011989 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 420662011990 Walker A motif; other site 420662011991 ATP binding site [chemical binding]; other site 420662011992 Walker B motif; other site 420662011993 arginine finger; other site 420662011994 Peptidase family M41; Region: Peptidase_M41; pfam01434 420662011995 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 420662011996 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 420662011997 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 420662011998 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 420662011999 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 420662012000 ATP binding site [chemical binding]; other site 420662012001 Mg2+ binding site [ion binding]; other site 420662012002 G-X-G motif; other site 420662012003 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 420662012004 Active Sites [active] 420662012005 Antimicrobial peptide resistance and lipid A acylation protein PagP; Region: PagP; cl06181 420662012006 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 420662012007 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 420662012008 ATP binding site [chemical binding]; other site 420662012009 putative Mg++ binding site [ion binding]; other site 420662012010 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 420662012011 nucleotide binding region [chemical binding]; other site 420662012012 P-loop Domain of unknown function (DUF2791); Region: DUF2791; pfam10923 420662012013 Domain of unknown function (DUF4016); Region: DUF4016; pfam13208 420662012014 tellurite resistance protein terB; Region: terB; cd07176 420662012015 putative metal binding site [ion binding]; other site 420662012016 Methyltransferase domain; Region: Methyltransf_27; pfam13708 420662012017 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 420662012018 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 420662012019 S-adenosylmethionine binding site [chemical binding]; other site 420662012020 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 420662012021 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 420662012022 Active Sites [active] 420662012023 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 420662012024 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 420662012025 cofactor binding site; other site 420662012026 DNA binding site [nucleotide binding] 420662012027 substrate interaction site [chemical binding]; other site 420662012028 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 420662012029 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 420662012030 putative active site [active] 420662012031 PhoH-like protein; Region: PhoH; pfam02562 420662012032 SprT homologues; Region: SprT; cl01182 420662012033 SprT-like family; Region: SprT-like; pfam10263 420662012034 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 420662012035 dimerization domain [polypeptide binding]; other site 420662012036 dimer interface [polypeptide binding]; other site 420662012037 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 420662012038 catalytic residues [active] 420662012039 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 420662012040 TraU protein; Region: TraU; pfam06834 420662012041 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; pfam09673 420662012042 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 420662012043 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 420662012044 dimer interface [polypeptide binding]; other site 420662012045 ssDNA binding site [nucleotide binding]; other site 420662012046 tetramer (dimer of dimers) interface [polypeptide binding]; other site 420662012047 replicative DNA helicase; Region: DnaB; TIGR00665 420662012048 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 420662012049 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 420662012050 Walker A motif; other site 420662012051 ATP binding site [chemical binding]; other site 420662012052 Walker B motif; other site 420662012053 DNA binding loops [nucleotide binding] 420662012054 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 420662012055 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 420662012056 active site 420662012057 metal binding site [ion binding]; metal-binding site 420662012058 interdomain interaction site; other site 420662012059 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 420662012060 AAA-like domain; Region: AAA_10; pfam12846 420662012061 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 420662012062 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 420662012063 ligand binding site [chemical binding]; other site 420662012064 TraL protein; Region: TraL; cl06278 420662012065 TraE protein; Region: TraE; cl05060 420662012066 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 420662012067 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 420662012068 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 420662012069 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 420662012070 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 420662012071 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 420662012072 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 420662012073 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 420662012074 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 420662012075 F plasmid transfer operon protein; Region: TraF; pfam13728 420662012076 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 420662012077 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 420662012078 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 420662012079 catalytic residues [active] 420662012080 hinge region; other site 420662012081 alpha helical domain; other site 420662012082 Type II/IV secretion system protein; Region: T2SE; pfam00437 420662012083 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 420662012084 Walker A motif; other site 420662012085 ATP binding site [chemical binding]; other site 420662012086 Walker B motif; other site 420662012087 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 420662012088 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 420662012089 N-acetyl-D-glucosamine binding site [chemical binding]; other site 420662012090 catalytic residue [active] 420662012091 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 420662012092 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 420662012093 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 420662012094 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 420662012095 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 420662012096 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 420662012097 active site 420662012098 dimer interface [polypeptide binding]; other site 420662012099 effector binding site; other site 420662012100 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 420662012101 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 420662012102 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 420662012103 generic binding surface I; other site 420662012104 generic binding surface II; other site 420662012105 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 420662012106 ATP binding site [chemical binding]; other site 420662012107 putative Mg++ binding site [ion binding]; other site 420662012108 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 420662012109 nucleotide binding region [chemical binding]; other site 420662012110 ATP-binding site [chemical binding]; other site 420662012111 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 420662012112 metal ion-dependent adhesion site (MIDAS); other site 420662012113 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 420662012114 Walker A motif; other site 420662012115 ATP binding site [chemical binding]; other site 420662012116 Protein of unknown function (DUF3150); Region: DUF3150; pfam11348 420662012117 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 420662012118 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 420662012119 DNA topoisomerase III; Provisional; Region: PRK07726 420662012120 active site 420662012121 putative interdomain interaction site [polypeptide binding]; other site 420662012122 putative metal-binding site [ion binding]; other site 420662012123 putative nucleotide binding site [chemical binding]; other site 420662012124 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 420662012125 DNA binding groove [nucleotide binding] 420662012126 domain I; other site 420662012127 phosphate binding site [ion binding]; other site 420662012128 domain II; other site 420662012129 domain III; other site 420662012130 nucleotide binding site [chemical binding]; other site 420662012131 catalytic site [active] 420662012132 domain IV; other site 420662012133 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 420662012134 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 420662012135 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 420662012136 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 420662012137 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 420662012138 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 420662012139 active site 420662012140 catalytic residues [active] 420662012141 Int/Topo IB signature motif; other site 420662012142 DNA binding site [nucleotide binding] 420662012143 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 420662012144 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 420662012145 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 420662012146 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 420662012147 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 420662012148 Walker A motif; other site 420662012149 ATP binding site [chemical binding]; other site 420662012150 Walker B motif; other site 420662012151 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 420662012152 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 420662012153 H-NS histone family; Region: Histone_HNS; pfam00816 420662012154 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 420662012155 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 420662012156 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 420662012157 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 420662012158 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662012159 DNA-binding site [nucleotide binding]; DNA binding site 420662012160 UTRA domain; Region: UTRA; pfam07702 420662012161 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 420662012162 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 420662012163 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 420662012164 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 420662012165 Walker A/P-loop; other site 420662012166 ATP binding site [chemical binding]; other site 420662012167 Q-loop/lid; other site 420662012168 ABC transporter signature motif; other site 420662012169 Walker B; other site 420662012170 D-loop; other site 420662012171 H-loop/switch region; other site 420662012172 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 420662012173 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 420662012174 dimer interface [polypeptide binding]; other site 420662012175 conserved gate region; other site 420662012176 putative PBP binding loops; other site 420662012177 ABC-ATPase subunit interface; other site 420662012178 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 420662012179 carbon-phosphorus lyase complex subunit; Validated; Region: phnH; PRK10147 420662012180 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 420662012181 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 420662012182 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 420662012183 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662012184 Walker A/P-loop; other site 420662012185 ATP binding site [chemical binding]; other site 420662012186 Q-loop/lid; other site 420662012187 ABC transporter signature motif; other site 420662012188 Walker B; other site 420662012189 D-loop; other site 420662012190 H-loop/switch region; other site 420662012191 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 420662012192 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 420662012193 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662012194 Walker A/P-loop; other site 420662012195 ATP binding site [chemical binding]; other site 420662012196 Q-loop/lid; other site 420662012197 ABC transporter signature motif; other site 420662012198 Walker B; other site 420662012199 D-loop; other site 420662012200 H-loop/switch region; other site 420662012201 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 420662012202 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 420662012203 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 420662012204 active site 420662012205 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 420662012206 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 420662012207 active site 420662012208 carbon-phosphorus lyase complex accessory protein; Provisional; Region: phnP; PRK11244 420662012209 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 420662012210 EamA-like transporter family; Region: EamA; cl17759 420662012211 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662012212 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 420662012213 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 420662012214 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 420662012215 catalytic triad [active] 420662012216 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 420662012217 active site 420662012218 SAM binding site [chemical binding]; other site 420662012219 homodimer interface [polypeptide binding]; other site 420662012220 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 420662012221 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 420662012222 putative active site [active] 420662012223 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 420662012224 putative active site [active] 420662012225 Precorrin-8X methylmutase; Region: CbiC; pfam02570 420662012226 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 420662012227 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 420662012228 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 420662012229 active site 420662012230 SAM binding site [chemical binding]; other site 420662012231 putative homodimer interface [polypeptide binding]; other site 420662012232 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 420662012233 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 420662012234 S-adenosylmethionine binding site [chemical binding]; other site 420662012235 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 420662012236 active site 420662012237 SAM binding site [chemical binding]; other site 420662012238 homodimer interface [polypeptide binding]; other site 420662012239 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 420662012240 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 420662012241 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 420662012242 Probable cobalt transporter subunit (CbtA); Region: CbtA; pfam09490 420662012243 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 420662012244 active site 420662012245 SAM binding site [chemical binding]; other site 420662012246 homodimer interface [polypeptide binding]; other site 420662012247 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 420662012248 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 420662012249 dimer interface [polypeptide binding]; other site 420662012250 [2Fe-2S] cluster binding site [ion binding]; other site 420662012251 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 420662012252 active site 420662012253 SAM binding site [chemical binding]; other site 420662012254 homodimer interface [polypeptide binding]; other site 420662012255 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 420662012256 FMN binding site [chemical binding]; other site 420662012257 dimer interface [polypeptide binding]; other site 420662012258 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662012259 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 420662012260 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 420662012261 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 420662012262 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662012263 DNA-binding site [nucleotide binding]; DNA binding site 420662012264 UTRA domain; Region: UTRA; pfam07702 420662012265 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 420662012266 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 420662012267 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 420662012268 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 420662012269 Walker A/P-loop; other site 420662012270 ATP binding site [chemical binding]; other site 420662012271 Q-loop/lid; other site 420662012272 ABC transporter signature motif; other site 420662012273 Walker B; other site 420662012274 D-loop; other site 420662012275 H-loop/switch region; other site 420662012276 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 420662012277 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 420662012278 dimer interface [polypeptide binding]; other site 420662012279 conserved gate region; other site 420662012280 putative PBP binding loops; other site 420662012281 ABC-ATPase subunit interface; other site 420662012282 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 420662012283 carbon-phosphorus lyase complex subunit; Validated; Region: phnH; PRK10147 420662012284 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 420662012285 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 420662012286 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 420662012287 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 420662012288 Walker A/P-loop; other site 420662012289 ATP binding site [chemical binding]; other site 420662012290 Q-loop/lid; other site 420662012291 ABC transporter signature motif; other site 420662012292 Walker B; other site 420662012293 D-loop; other site 420662012294 H-loop/switch region; other site 420662012295 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 420662012296 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 420662012297 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 420662012298 Walker A/P-loop; other site 420662012299 ATP binding site [chemical binding]; other site 420662012300 Q-loop/lid; other site 420662012301 ABC transporter signature motif; other site 420662012302 Walker B; other site 420662012303 D-loop; other site 420662012304 H-loop/switch region; other site 420662012305 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 420662012306 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 420662012307 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 420662012308 active site 420662012309 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 420662012310 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 420662012311 active site 420662012312 carbon-phosphorus lyase complex accessory protein; Provisional; Region: phnP; PRK11244 420662012313 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 420662012314 EamA-like transporter family; Region: EamA; cl17759 420662012315 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 420662012316 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 420662012317 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 420662012318 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 420662012319 catalytic triad [active] 420662012320 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 420662012321 active site 420662012322 SAM binding site [chemical binding]; other site 420662012323 homodimer interface [polypeptide binding]; other site 420662012324 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 420662012325 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 420662012326 putative active site [active] 420662012327 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 420662012328 putative active site [active] 420662012329 Precorrin-8X methylmutase; Region: CbiC; pfam02570 420662012330 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 420662012331 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 420662012332 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 420662012333 active site 420662012334 SAM binding site [chemical binding]; other site 420662012335 putative homodimer interface [polypeptide binding]; other site 420662012336 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 420662012337 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 420662012338 S-adenosylmethionine binding site [chemical binding]; other site 420662012339 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 420662012340 active site 420662012341 SAM binding site [chemical binding]; other site 420662012342 homodimer interface [polypeptide binding]; other site 420662012343 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 420662012344 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 420662012345 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 420662012346 Probable cobalt transporter subunit (CbtA); Region: CbtA; pfam09490 420662012347 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 420662012348 active site 420662012349 SAM binding site [chemical binding]; other site 420662012350 homodimer interface [polypeptide binding]; other site 420662012351 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 420662012352 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 420662012353 dimer interface [polypeptide binding]; other site 420662012354 [2Fe-2S] cluster binding site [ion binding]; other site 420662012355 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 420662012356 active site 420662012357 SAM binding site [chemical binding]; other site 420662012358 homodimer interface [polypeptide binding]; other site 420662012359 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 420662012360 FMN binding site [chemical binding]; other site 420662012361 dimer interface [polypeptide binding]; other site 420662012362 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662012363 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 420662012364 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 420662012365 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 420662012366 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 420662012367 dimer interface [polypeptide binding]; other site 420662012368 phosphorylation site [posttranslational modification] 420662012369 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 420662012370 ATP binding site [chemical binding]; other site 420662012371 Mg2+ binding site [ion binding]; other site 420662012372 G-X-G motif; other site 420662012373 Response regulator receiver domain; Region: Response_reg; pfam00072 420662012374 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 420662012375 active site 420662012376 phosphorylation site [posttranslational modification] 420662012377 intermolecular recognition site; other site 420662012378 dimerization interface [polypeptide binding]; other site 420662012379 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662012380 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 420662012381 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 420662012382 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2; Region: FDH_like_2; cd08284 420662012383 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 420662012384 catalytic Zn binding site [ion binding]; other site 420662012385 NAD(P) binding site [chemical binding]; other site 420662012386 structural Zn binding site [ion binding]; other site 420662012387 malate dehydrogenase; Reviewed; Region: PRK06223 420662012388 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 420662012389 LDH/MDH dimer interface [polypeptide binding]; other site 420662012390 NAD(P) binding site [chemical binding]; other site 420662012391 substrate binding site [chemical binding]; other site 420662012392 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1; Region: BMC_like_1_repeat1; cd07051 420662012393 putative hexamer interface [polypeptide binding]; other site 420662012394 putative hexagonal pore; other site 420662012395 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 2; Region: BMC_like_1_repeat2; cd07052 420662012396 putative hexamer interface [polypeptide binding]; other site 420662012397 putative hexagonal pore; other site 420662012398 ethanolamine utilization protein EutJ; Provisional; Region: PRK15080 420662012399 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 420662012400 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 420662012401 putative catalytic cysteine [active] 420662012402 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 420662012403 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 420662012404 Hexamer interface [polypeptide binding]; other site 420662012405 Putative hexagonal pore residue; other site 420662012406 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 420662012407 Hexamer/Pentamer interface [polypeptide binding]; other site 420662012408 central pore; other site 420662012409 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 420662012410 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 420662012411 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 420662012412 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 420662012413 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 420662012414 Hexamer interface [polypeptide binding]; other site 420662012415 Hexagonal pore residue; other site 420662012416 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 420662012417 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 420662012418 N-terminal plug; other site 420662012419 ligand-binding site [chemical binding]; other site 420662012420 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 420662012421 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 420662012422 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 420662012423 conserved cys residue [active] 420662012424 Cobinamide kinase / cobinamide phosphate guanyltransferase; Region: CobU; cl17363 420662012425 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 420662012426 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 420662012427 intersubunit interface [polypeptide binding]; other site 420662012428 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 420662012429 dimer interface [polypeptide binding]; other site 420662012430 putative PBP binding regions; other site 420662012431 ABC-ATPase subunit interface; other site 420662012432 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 420662012433 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 420662012434 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 420662012435 Walker A/P-loop; other site 420662012436 ATP binding site [chemical binding]; other site 420662012437 Q-loop/lid; other site 420662012438 ABC transporter signature motif; other site 420662012439 Walker B; other site 420662012440 D-loop; other site 420662012441 H-loop/switch region; other site 420662012442 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 420662012443 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 420662012444 homodimer interface [polypeptide binding]; other site 420662012445 Walker A motif; other site 420662012446 ATP binding site [chemical binding]; other site 420662012447 hydroxycobalamin binding site [chemical binding]; other site 420662012448 Walker B motif; other site 420662012449 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 420662012450 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 420662012451 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 420662012452 catalytic residue [active] 420662012453 cobyric acid synthase; Provisional; Region: PRK00784 420662012454 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 420662012455 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 420662012456 conserved cys residue [active] 420662012457 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 420662012458 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 420662012459 putative dimer interface [polypeptide binding]; other site 420662012460 active site pocket [active] 420662012461 putative cataytic base [active] 420662012462 cobalamin synthase; Reviewed; Region: cobS; PRK00235 420662012463 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 420662012464 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 420662012465 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 420662012466 Methylmalonic aciduria and homocystinuria type C protein and similar proteins; Region: MMACHC-like; cd12959 420662012467 dimer interface [polypeptide binding]; other site 420662012468 cobalamin binding site [chemical binding]; other site 420662012469 Transposase; Region: HTH_Tnp_1; cl17663 420662012470 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662012471 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 420662012472 N-terminal domain interface [polypeptide binding]; other site 420662012473 Homeodomain-like domain; Region: HTH_23; pfam13384 420662012474 Winged helix-turn helix; Region: HTH_29; pfam13551 420662012475 Homeodomain-like domain; Region: HTH_32; pfam13565 420662012476 DDE superfamily endonuclease; Region: DDE_3; pfam13358 420662012477 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 420662012478 Transposase, Mutator family; Region: Transposase_mut; pfam00872 420662012479 MULE transposase domain; Region: MULE; pfam10551 420662012480 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 420662012481 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 420662012482 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 420662012483 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 420662012484 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 420662012485 Transcriptional regulators [Transcription]; Region: GntR; COG1802 420662012486 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 420662012487 DNA-binding site [nucleotide binding]; DNA binding site 420662012488 FCD domain; Region: FCD; pfam07729 420662012489 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 420662012490 B12 binding site [chemical binding]; other site 420662012491 cobalt ligand [ion binding]; other site 420662012492 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 420662012493 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662012494 acyl-activating enzyme (AAE) consensus motif; other site 420662012495 AMP binding site [chemical binding]; other site 420662012496 active site 420662012497 CoA binding site [chemical binding]; other site 420662012498 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 420662012499 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 420662012500 Walker A; other site 420662012501 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM...; Region: MM_CoA_mutase_ICM_like; cd03680 420662012502 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 420662012503 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 420662012504 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 420662012505 PYR/PP interface [polypeptide binding]; other site 420662012506 dimer interface [polypeptide binding]; other site 420662012507 TPP binding site [chemical binding]; other site 420662012508 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 420662012509 Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL...; Region: TPP_BZL_OCoD_HPCL; cd02004 420662012510 TPP-binding site; other site 420662012511 dimer interface [polypeptide binding]; other site 420662012512 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 420662012513 trimer interface [polypeptide binding]; other site 420662012514 putative metal binding site [ion binding]; other site 420662012515 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 420662012516 trimer interface [polypeptide binding]; other site 420662012517 putative metal binding site [ion binding]; other site 420662012518 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 420662012519 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 420662012520 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 420662012521 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 420662012522 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 420662012523 putative transposase OrfB; Reviewed; Region: PHA02517 420662012524 HTH-like domain; Region: HTH_21; pfam13276 420662012525 Integrase core domain; Region: rve; pfam00665 420662012526 Integrase core domain; Region: rve_3; pfam13683 420662012527 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662012528 Transposase; Region: HTH_Tnp_1; pfam01527 420662012529 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 420662012530 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 420662012531 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 420662012532 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 420662012533 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 420662012534 FMN-binding pocket [chemical binding]; other site 420662012535 flavin binding motif; other site 420662012536 phosphate binding motif [ion binding]; other site 420662012537 beta-alpha-beta structure motif; other site 420662012538 NAD binding pocket [chemical binding]; other site 420662012539 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 420662012540 catalytic loop [active] 420662012541 iron binding site [ion binding]; other site 420662012542 Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3; Region: Rieske_RO_Alpha_PhDO_like; cd03479 420662012543 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 420662012544 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 420662012545 hydrophobic ligand binding site; other site 420662012546 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 420662012547 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 420662012548 HIT family signature motif; other site 420662012549 catalytic residue [active] 420662012550 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 420662012551 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 420662012552 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 420662012553 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 420662012554 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 420662012555 catalytic core [active] 420662012556 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 420662012557 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662012558 acyl-activating enzyme (AAE) consensus motif; other site 420662012559 active site 420662012560 AMP binding site [chemical binding]; other site 420662012561 CoA binding site [chemical binding]; other site 420662012562 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 420662012563 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 420662012564 Walker A/P-loop; other site 420662012565 ATP binding site [chemical binding]; other site 420662012566 Q-loop/lid; other site 420662012567 ABC transporter signature motif; other site 420662012568 Walker B; other site 420662012569 D-loop; other site 420662012570 H-loop/switch region; other site 420662012571 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 420662012572 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 420662012573 putative ligand binding site [chemical binding]; other site 420662012574 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; cl00454 420662012575 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 420662012576 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 420662012577 TM-ABC transporter signature motif; other site 420662012578 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 420662012579 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 420662012580 Walker A/P-loop; other site 420662012581 ATP binding site [chemical binding]; other site 420662012582 Q-loop/lid; other site 420662012583 ABC transporter signature motif; other site 420662012584 Walker B; other site 420662012585 D-loop; other site 420662012586 H-loop/switch region; other site 420662012587 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 420662012588 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 420662012589 putative transposase OrfB; Reviewed; Region: PHA02517 420662012590 HTH-like domain; Region: HTH_21; pfam13276 420662012591 Integrase core domain; Region: rve; pfam00665 420662012592 Integrase core domain; Region: rve_3; pfam13683 420662012593 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662012594 Transposase; Region: HTH_Tnp_1; pfam01527 420662012595 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 420662012596 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 420662012597 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 420662012598 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662012599 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662012600 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cd00531 420662012601 SnoaL-like domain; Region: SnoaL_3; pfam13474 420662012602 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662012603 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662012604 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 420662012605 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 420662012606 Transposase; Region: HTH_Tnp_1; pfam01527 420662012607 putative transposase OrfB; Reviewed; Region: PHA02517 420662012608 HTH-like domain; Region: HTH_21; pfam13276 420662012609 Integrase core domain; Region: rve; pfam00665 420662012610 Integrase core domain; Region: rve_3; pfam13683 420662012611 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662012612 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662012613 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 420662012614 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 420662012615 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 420662012616 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 420662012617 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 420662012618 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 420662012619 AAA ATPase domain; Region: AAA_16; pfam13191 420662012620 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 420662012621 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 420662012622 DNA binding residues [nucleotide binding] 420662012623 dimerization interface [polypeptide binding]; other site 420662012624 Rubredoxin [Energy production and conversion]; Region: COG1773 420662012625 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 420662012626 iron binding site [ion binding]; other site 420662012627 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 420662012628 Rubredoxin; Region: Rubredoxin; pfam00301 420662012629 iron binding site [ion binding]; other site 420662012630 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 420662012631 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 420662012632 substrate binding pocket [chemical binding]; other site 420662012633 Transposase domain (DUF772); Region: DUF772; pfam05598 420662012634 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 420662012635 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 420662012636 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 420662012637 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 420662012638 Fatty acid desaturase; Region: FA_desaturase; pfam00487 420662012639 Di-iron ligands [ion binding]; other site 420662012640 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662012641 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662012642 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 420662012643 GAF domain; Region: GAF; pfam01590 420662012644 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 420662012645 Walker A motif; other site 420662012646 ATP binding site [chemical binding]; other site 420662012647 Walker B motif; other site 420662012648 arginine finger; other site 420662012649 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 420662012650 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 420662012651 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 420662012652 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 420662012653 hypothetical protein; Validated; Region: PRK07581 420662012654 RmuC family; Region: RmuC; pfam02646 420662012655 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 420662012656 putative active site [active] 420662012657 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 420662012658 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 420662012659 Uncharacterized conserved protein [Function unknown]; Region: COG4544 420662012660 DNA Polymerase Y-family; Region: PolY_like; cd03468 420662012661 DNA binding site [nucleotide binding] 420662012662 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 420662012663 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 420662012664 putative active site [active] 420662012665 putative PHP Thumb interface [polypeptide binding]; other site 420662012666 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 420662012667 generic binding surface I; other site 420662012668 generic binding surface II; other site 420662012669 Uncharacterized distant relative of cell wall-associated hydrolases [Function unknown]; Region: COG3863 420662012670 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 420662012671 RNA binding site [nucleotide binding]; other site 420662012672 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 420662012673 metal ion-dependent adhesion site (MIDAS); other site 420662012674 Protein of unknown function (DUF3620); Region: DUF3620; pfam12281 420662012675 Ligand Binding Domain of Ephrin Receptors; Region: EphR_LBD; cl02704