-- dump date 20111121_011513 -- class Genbank::misc_feature -- table misc_feature_note -- id note 543891000001 The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible...; Region: CooC; cd02034 543891000002 P-loop; other site 543891000003 Transcriptional activator TraM; Region: Activator-TraM; cl11943 543891000004 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional; Region: PRK09522 543891000005 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 543891000006 ParB-like partition proteins; Region: parB_part; TIGR00180 543891000007 ParB-like nuclease domain; Region: ParBc; cl02129 543891000008 KorB domain; Region: KorB; pfam08535 543891000009 KorB C-terminal beta-barrel domain; Region: KorB_C; pfam06613 543891000010 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...; Region: ParA; cd02042 543891000011 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 543891000012 P-loop; other site 543891000013 Magnesium ion binding site; other site 543891000014 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...; Region: ParA; cd02042 543891000015 Magnesium ion binding site; other site 543891000016 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...; Region: ParA; cd02042 543891000017 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 543891000018 P-loop; other site 543891000019 Magnesium ion binding site; other site 543891000020 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...; Region: ParA; cd02042 543891000021 Magnesium ion binding site; other site 543891000022 conjugal transfer protein TrbA; Provisional; Region: PRK13890 543891000023 Protein of unknown function (DUF2761); Region: DUF2761; pfam10959 543891000024 Antirestriction protein; Region: Antirestrict; pfam03230 543891000025 RelB antitoxin; Region: RelB; cl01171 543891000026 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 543891000027 Transposase; Region: Transposase_7; pfam01526 543891000028 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 543891000029 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 543891000030 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 543891000031 multiple promoter invertase; Provisional; Region: mpi; PRK13413 543891000032 catalytic residues; other site 543891000033 catalytic nucleophile; other site 543891000034 Presynaptic Site I dimer interface; other site 543891000035 Synaptic Antiparallel dimer interface; other site 543891000036 Synaptic Flat tetramer interface; other site 543891000037 Synaptic Site I dimer interface; other site 543891000038 DNA binding site 543891000039 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 543891000040 DNA-binding interface; DNA binding site 543891000041 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 543891000042 Chromate transporter; Region: Chromate_transp; cl00902 543891000043 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 543891000044 Chromate transporter; Region: Chromate_transp; cl00902 543891000045 Replication initiator protein A; Region: RPA; cl02339 543891000046 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 543891000047 dimer interface; other site 543891000048 ssDNA binding site; other site 543891000049 tetramer (dimer of dimers) interface; other site 543891000050 conjugal transfer protein TrbA; Provisional; Region: PRK13890 543891000051 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 543891000052 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 543891000053 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...; Region: VirB11-like_ATPase; cd01130 543891000054 ATP binding site; other site 543891000055 Walker A motif; other site 543891000056 hexamer interface; other site 543891000057 Walker B motif; other site 543891000058 TrbC/VIRB2 family; Region: TrbC; cl01583 543891000059 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 543891000060 conjugal transfer protein TrbE; Provisional; Region: PRK13891 543891000061 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 543891000062 VirB8 protein; Region: VirB8; cl01500 543891000063 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 543891000064 VirB7 interaction site; other site 543891000065 conjugal transfer protein TrbH; Provisional; Region: PRK13883 543891000066 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 543891000067 Conjugal transfer protein TrbH; Region: TrbH; pfam07283 543891000068 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 543891000069 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 543891000070 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 543891000071 TrbM; Region: TrbM; cl06455 543891000072 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 catalyze...; Region: LT_GEWL; cd00254 543891000073 N-acetyl-D-glucosamine binding site; other site 543891000074 catalytic residue; other site 543891000075 TraX protein; Region: TraX; cl05434 543891000076 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 543891000077 ligand binding site; other site 543891000078 Transposase; Region: Transposase_7; pfam01526 543891000079 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 543891000080 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 543891000081 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; cl11426 543891000082 amidohydrolase, AtzE family; Region: amido_AtzE; TIGR02715 543891000083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 543891000084 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 543891000085 active site 1 543891000086 dimer interface; other site 543891000087 hexamer interface; other site 543891000088 active site 2 543891000089 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 543891000090 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 543891000091 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 543891000092 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 543891000093 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 543891000094 NAD binding site; other site 543891000095 catalytic residues; other site 543891000096 mutated transporter gene; nonfunctional 543891000097 The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol; Region: 2A5CPDO_A; cd07373 543891000098 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 543891000099 The beta subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol; Region: 2A5CPDO_B; cd07372 543891000100 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 543891000101 putative active site; other site 543891000102 putative metal binding site; other site 543891000103 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 543891000104 homotrimer interaction site; other site 543891000105 putative active site; other site 543891000106 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 543891000107 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl01383 543891000108 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 543891000109 active site 543891000110 Muconolactone delta-isomerase; Region: MIase; cl01992 543891000111 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-...; Region: MLE; cd03318 543891000112 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 543891000113 octamer interface; other site 543891000114 active site 543891000115 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 543891000116 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 543891000117 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; Region: PBP2_BenM_CatM_CatR; cd08445 543891000118 dimerizarion interface; other site 543891000119 CrgA pocket; other site 543891000120 substrate binding pocket; other site 543891000121 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 543891000122 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 543891000123 Transcriptional regulators [Transcription]; Region: GntR; COG1802 543891000124 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 543891000125 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 543891000126 NAD(P) binding site; other site 543891000127 catalytic residues; other site 543891000128 transposase based on nucleotide sequence but unknown protein based on predicted amino acids 543891000129 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 543891000130 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 543891000131 dimer interface; other site 543891000132 putative tRNA-binding site; other site 543891000133 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 543891000134 dimer interface; other site 543891000135 FMN binding site; other site 543891000136 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 543891000137 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 543891000138 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 543891000139 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; cl12031 543891000140 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a...; Region: Nitroreductase; cd02136 543891000141 putative FMN binding site; other site 543891000142 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 543891000143 Putative transposase; Region: Transposase_32; pfam04986 543891000144 Domain of unknown function; Region: DUF300; pfam03619 543891000145 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 543891000146 catalytic residues; other site 543891000147 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 543891000148 transmembrane helices; other site 543891000149 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 543891000150 Low molecular weight phosphatase family; Region: LMWPc; cd00115 543891000151 active site 543891000152 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 543891000153 putative DNA binding site; other site 543891000154 putative Zn2+ binding site; other site 543891000155 dimerization interface; other site 543891000156 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 543891000157 Putative transposase; Region: Transposase_32; pfam04986 543891000158 Transposase; Region: Transposase_7; pfam01526 543891000159 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 543891000160 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 543891000161 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 543891000162 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 543891000163 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication...; Region: TOPRIM_primases; cd01029 543891000164 active site 543891000165 metal-binding site 543891000166 interdomain interaction site; other site 543891000167 DNA topoisomerase III; Provisional; Region: PRK07726 543891000168 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:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 543891000169 active site 543891000170 putative interdomain interaction site; other site 543891000171 putative metal-binding site; other site 543891000172 putative nucleotide binding site; other site 543891000173 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...; Region: TOP1Ac; cd00186 543891000174 domain I; other site 543891000175 DNA binding groove 543891000176 phosphate binding site; other site 543891000177 domain II; other site 543891000178 domain III; other site 543891000179 nucleotide binding site; other site 543891000180 catalytic site; other site 543891000181 domain IV; other site 543891000182 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 543891000183 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88)...; Region: Peptidase_S24_S26; cl10465 543891000184 Peptidase S26; Region: Peptidase_S26; pfam10502 543891000185 TraG/TraD family; Region: TraG; pfam02534 543891000186 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 543891000187 Walker A motif; other site 543891000188 ATP binding site; other site 543891000189 Walker B motif; other site 543891000190 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 543891000191 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 543891000192 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 688245000193 hypothetical protein; Validated; Region: PRK06672 688245000194 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 688245000195 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...; Region: AAA; cd00009 688245000196 Walker A motif; other site 688245000197 ATP binding site; other site 688245000198 Walker B motif; other site 688245000199 arginine finger; other site 688245000200 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 688245000201 DnaA box-binding interface; other site 688245000202 DNA polymerase III subunit beta; Validated; Region: PRK05643 688245000203 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...; Region: beta_clamp; cd00140 688245000204 putative DNA binding surface; other site 688245000205 dimer interface; other site 688245000206 beta-clamp/clamp loader binding surface; other site 688245000207 beta-clamp/translesion DNA polymerase binding surface; other site 688245000208 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 688245000209 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 688245000210 ATP binding site; other site 688245000211 Mg2+ binding site; other site 688245000212 G-X-G motif; other site 688245000213 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 688245000214 anchoring element; other site 688245000215 dimer interface; other site 688245000216 ATP binding site; other site 688245000217 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 688245000218 active site 688245000219 putative metal-binding site; other site 688245000220 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 688245000221 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000222 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 688245000223 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245000224 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000225 NAD(P) binding site; other site 688245000226 active site 688245000227 Putative cyclase; Region: Cyclase; cl00814 688245000228 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 688245000229 DUF35 OB-fold domain; Region: DUF35; pfam01796 688245000230 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000231 NAD(P) binding site; other site 688245000232 active site 688245000233 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 3-ketacyl-; Region: SCP-x_thiolase; cd00829 688245000234 acetyl-CoA acetyltransferase; Provisional; Region: PRK12578 688245000235 active site 688245000236 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 688245000237 crotonobetaine/carnitine-CoA ligase; Provisional; Region: PRK06155 688245000238 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245000239 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 688245000240 inter-subunit interface; other site 688245000241 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 688245000242 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)...; Region: Rieske; cl00938 688245000243 iron-sulfur cluster; other site 688245000244 [2Fe-2S] cluster binding site; other site 688245000245 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 688245000246 putative alpha subunit interface; other site 688245000247 putative active site; other site 688245000248 putative substrate binding site; other site 688245000249 Fe binding site; other site 688245000250 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 688245000251 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245000252 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...; Region: PDR_like; cd06185 688245000253 FMN-binding pocket; other site 688245000254 flavin binding motif; other site 688245000255 phosphate binding motif; other site 688245000256 beta-alpha-beta structure motif; other site 688245000257 NAD binding pocket; other site 688245000258 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 688245000259 catalytic loop; other site 688245000260 iron binding site; other site 688245000261 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 688245000262 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 688245000263 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 688245000264 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 688245000265 dimer interface; other site 688245000266 PYR/PP interface; other site 688245000267 TPP binding site; other site 688245000268 substrate binding site; other site 688245000269 TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the...; Region: TPP_IOR_alpha; cd02008 688245000270 TPP-binding site; other site 688245000271 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 688245000272 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245000273 C-terminal domain interface; other site 688245000274 GSH binding site (G-site); other site 688245000275 dimer interface; other site 688245000276 GST_C 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_C_Beta; cd03188 688245000277 dimer interface; other site 688245000278 N-terminal domain interface; other site 688245000279 substrate binding pocket (H-site); other site 688245000280 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 688245000281 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245000282 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245000283 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 688245000284 ATP binding site; other site 688245000285 Mg2+ binding site; other site 688245000286 G-X-G motif; other site 688245000287 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245000288 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 688245000289 active site 688245000290 phosphorylation site 688245000291 intermolecular recognition site; other site 688245000292 dimerization interface; other site 688245000293 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...; Region: trans_reg_C; cd00383 688245000294 DNA binding site 688245000295 Outer membrane efflux protein; Region: OEP; pfam02321 688245000296 Outer membrane efflux protein; Region: OEP; pfam02321 688245000297 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 688245000298 pyruvate carboxylase; Reviewed; Region: PRK12999 688245000299 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 688245000300 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 688245000301 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; cl12029 688245000302 CRISPR/Cas system-associated DinG family helicase Csf4; Region: csf4_Type-U; cl09250 688245000303 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 688245000304 Domain of Unknown Function (DUF1520); Region: DUF1520; pfam07480 688245000305 Putative exonuclease, RdgC; Region: RdgC; cl01122 688245000306 beta-ketothiolase; Provisional; Region: PRK09051 688245000307 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 688245000308 dimer interface; other site 688245000309 active site 688245000310 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 688245000311 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 688245000312 DNA binding residues 688245000313 dimer interface; other site 688245000314 copper binding site; other site 688245000315 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 688245000316 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245000317 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245000318 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245000319 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 688245000320 FMN binding site; other site 688245000321 active site 688245000322 substrate binding site; other site 688245000323 catalytic residue; other site 688245000324 glutathionine S-transferase; Provisional; Region: PRK10542 688245000325 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 688245000326 C-terminal domain interface; other site 688245000327 GSH binding site (G-site); other site 688245000328 dimer interface; other site 688245000329 GST_C 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_C_Beta; cd03188 688245000330 N-terminal domain interface; other site 688245000331 dimer interface; other site 688245000332 substrate binding pocket (H-site); other site 688245000333 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245000334 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 688245000335 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 688245000336 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; cl12011 688245000337 LysE type translocator; Region: LysE; cl00565 688245000338 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 688245000339 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...; Region: ParA; cd02042 688245000340 P-loop; other site 688245000341 Magnesium ion binding site; other site 688245000342 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245000343 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...; Region: ParA; cd02042 688245000344 Magnesium ion binding site; other site 688245000345 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; cl12031 688245000346 ParB-like partition proteins; Region: parB_part; TIGR00180 688245000347 ParB-like nuclease domain; Region: ParBc; cl02129 688245000348 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 688245000349 intersubunit interface; other site 688245000350 active site 688245000351 Zn2+ binding site; other site 688245000352 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245000353 hypothetical protein; Provisional; Region: PRK07338 688245000354 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 688245000355 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245000356 putative substrate translocation pore; other site 688245000357 Cupin domain; Region: Cupin_2; cl09118 688245000358 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245000359 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 688245000360 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245000361 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...; Region: Sigma70_r4; cd06171 688245000362 DNA binding residues 688245000363 sulfite oxidase; Provisional; Region: PLN00177 688245000364 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 688245000365 Moco binding site; other site 688245000366 metal coordination site; other site 688245000367 dimerization interface; other site 688245000368 Cytochrome c; Region: Cytochrom_C; cl11414 688245000369 Sel1 repeat; Region: Sel1; cl02723 688245000370 D-lactate dehydrogenase [cytochrome]; Region: PLN02805 688245000371 FAD binding domain; Region: FAD_binding_4; pfam01565 688245000372 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 688245000373 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 688245000374 putative ligand binding site; other site 688245000375 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...; Region: EFh; cd00051 688245000376 Ca2+ binding site; other site 688245000377 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 688245000378 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 688245000379 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000380 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 688245000381 dimerization interface; other site 688245000382 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245000383 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 688245000384 potential frameshift: common BLAST hit: gi|160895520|ref|YP_001561102.1| extracellular solute-binding protein 688245000385 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...; Region: PBPb; cd00134 688245000386 substrate binding pocket; other site 688245000387 membrane-bound complex binding site; other site 688245000388 hinge residues; other site 688245000389 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 688245000390 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245000391 aspartate racemase; Region: asp_race; TIGR00035 688245000392 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245000393 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 688245000394 4Fe-4S binding domain; Region: Fer4; pfam00037 688245000395 These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer...; Region: CYPOR_like_FNR; cd06208 688245000396 dimerization interface; other site 688245000397 FAD binding pocket; other site 688245000398 FAD binding motif; other site 688245000399 catalytic residues; other site 688245000400 NAD binding pocket; other site 688245000401 phosphate binding motif; other site 688245000402 beta-alpha-beta structure motif; other site 688245000403 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 688245000404 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 688245000405 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 688245000406 substrate binding site; other site 688245000407 oxyanion hole (OAH) forming residues; other site 688245000408 trimer interface; other site 688245000409 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; cl14780 688245000410 substrate binding site; other site 688245000411 trimer interface; other site 688245000412 oxyanion hole (OAH) forming residues; other site 688245000413 threonine dehydratase; Provisional; Region: PRK07334 688245000414 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 688245000415 tetramer interface; other site 688245000416 pyridoxal 5'-phosphate binding site; other site 688245000417 catalytic residue; other site 688245000418 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 688245000419 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 688245000420 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 688245000421 Phosphoenolpyruvate carboxykinase; Region: PEPCK; pfam00821 688245000422 active site 688245000423 substrate-binding site; other site 688245000424 metal-binding site 688245000425 GTP binding site; other site 688245000426 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245000427 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000428 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 688245000429 substrate binding pocket; other site 688245000430 dimerization interface; other site 688245000431 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245000432 active site 688245000433 metal-binding site 688245000434 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 688245000435 Ligand Binding Site; other site 688245000436 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 688245000437 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000438 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 688245000439 dimerization interface; other site 688245000440 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245000441 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 688245000442 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000443 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245000444 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245000445 Flavin Reductases; Region: FlaRed; cl00801 688245000446 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 688245000447 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245000448 glutathione reductase; Validated; Region: PRK06116 688245000449 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245000450 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 688245000451 Septum formation topological specificity factor MinE; Region: MinE; cl00538 688245000452 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 688245000453 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...; Region: MinD; cd02036 688245000454 Switch I; other site 688245000455 Switch II; other site 688245000456 septum formation inhibitor; Reviewed; Region: PRK01973 688245000457 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 688245000458 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 688245000459 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 688245000460 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 688245000461 substrate binding site; other site 688245000462 oxyanion hole (OAH) forming residues; other site 688245000463 trimer interface; other site 688245000464 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 688245000465 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 688245000466 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245000467 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245000468 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 688245000469 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 688245000470 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; cl14056 688245000471 Permease family; Region: Xan_ur_permease; cl00967 688245000472 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 688245000473 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 688245000474 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 688245000475 CoenzymeA binding site; other site 688245000476 subunit interaction site; other site 688245000477 PHB binding site; other site 688245000478 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245000479 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245000480 Walker A/P-loop; other site 688245000481 ATP binding site; other site 688245000482 Q-loop/lid; other site 688245000483 ABC transporter signature motif; other site 688245000484 Walker B; other site 688245000485 D-loop; other site 688245000486 H-loop/switch region; other site 688245000487 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245000488 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245000489 Walker A/P-loop; other site 688245000490 ATP binding site; other site 688245000491 Q-loop/lid; other site 688245000492 ABC transporter signature motif; other site 688245000493 Walker B; other site 688245000494 D-loop; other site 688245000495 H-loop/switch region; other site 688245000496 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 688245000497 TM-ABC transporter signature motif; other site 688245000498 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 688245000499 TM-ABC transporter signature motif; other site 688245000500 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245000501 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 688245000502 putative ligand binding site; other site 688245000503 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 688245000504 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245000505 aldehyde dehydrogenase; Provisional; Region: PRK11903 688245000506 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 688245000507 NAD(P) binding site; other site 688245000508 catalytic residues; other site 688245000509 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 688245000510 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...; Region: SK; cd00464 688245000511 ADP binding site; other site 688245000512 magnesium binding site; other site 688245000513 putative shikimate binding site; other site 688245000514 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 688245000515 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245000516 active site 688245000517 Peptidase family M48; Region: Peptidase_M48; cl12018 688245000518 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245000519 EamA-like transporter family; Region: EamA; cl01037 688245000520 Cupin domain; Region: Cupin_2; cl09118 688245000521 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245000522 muropeptide transporter; Reviewed; Region: ampG; PRK11902 688245000523 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; cl11420 688245000524 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245000525 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 688245000526 active site 688245000527 phosphorylation site 688245000528 intermolecular recognition site; other site 688245000529 dimerization interface; other site 688245000530 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...; Region: trans_reg_C; cd00383 688245000531 DNA binding site 688245000532 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245000533 dimerization interface; other site 688245000534 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 trans...; Region: HisKA; cd00082 688245000535 dimer interface; other site 688245000536 phosphorylation site 688245000537 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 688245000538 ATP binding site; other site 688245000539 Mg2+ binding site; other site 688245000540 G-X-G motif; other site 688245000541 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 688245000542 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000543 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 688245000544 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 688245000545 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 688245000546 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 688245000547 putative NAD(P) binding site; other site 688245000548 active site 688245000549 putative substrate binding site; other site 688245000550 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 688245000551 Transposase DDE domain; Region: Transposase_11; pfam01609 688245000552 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 688245000553 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 688245000554 Ligand binding site; other site 688245000555 Putative Catalytic site; other site 688245000556 DXD motif; other site 688245000557 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 688245000558 O-Antigen ligase; Region: Wzy_C; cl04850 688245000559 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 688245000560 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 688245000561 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 688245000562 putative ADP-binding pocket; other site 688245000563 Zinc-finger domain; Region: zf-CHCC; cl01821 688245000564 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 alpha-...; Region: BCAT_beta_family; cd01557 688245000565 homodimer interface; other site 688245000566 substrate-cofactor binding pocket; other site 688245000567 Aminotransferase class IV; Region: Aminotran_4; pfam01063 688245000568 catalytic residue; other site 688245000569 DNA repair protein RadA; Provisional; Region: PRK11823 688245000570 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 688245000571 Walker A motif/ATP binding site; other site 688245000572 ATP binding site; other site 688245000573 Walker B motif; other site 688245000574 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 688245000575 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 688245000576 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 688245000577 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 688245000578 NAD(P) binding site; other site 688245000579 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245000580 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 688245000581 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245000582 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000583 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 688245000584 dimerization interface; other site 688245000585 Predicted membrane protein [Function unknown]; Region: COG4125 688245000586 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 688245000587 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 688245000588 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; cl12073 688245000589 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 688245000590 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 688245000591 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 688245000592 substrate binding pocket; other site 688245000593 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 688245000594 B12 binding site; other site 688245000595 cobalt ligand; other site 688245000596 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 688245000597 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245000598 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000599 DNA binding site 688245000600 FCD domain; Region: FCD; cl11656 688245000601 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 688245000602 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 688245000603 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245000604 active site 688245000605 signature motif; other site 688245000606 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245000607 active site 688245000608 signature motif; other site 688245000609 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 688245000610 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 688245000611 active site 688245000612 catalytic site; other site 688245000613 tryptophan synthase, beta chain; Region: PLN02618 688245000614 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 688245000615 pyridoxal 5'-phosphate binding site; other site 688245000616 catalytic residue; other site 688245000617 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 688245000618 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 688245000619 G1 box; other site 688245000620 GTP/Mg2+ binding site; other site 688245000621 Switch I region; other site 688245000622 G2 box; other site 688245000623 Switch II region; other site 688245000624 G3 box; other site 688245000625 G4 box; other site 688245000626 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245000627 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 trans-...; Region: HisKA; cl00080 688245000628 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 688245000629 ATP binding site; other site 688245000630 Mg2+ binding site; other site 688245000631 G-X-G motif; other site 688245000632 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245000633 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 688245000634 active site 688245000635 phosphorylation site 688245000636 intermolecular recognition site; other site 688245000637 dimerization interface; other site 688245000638 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...; Region: trans_reg_C; cd00383 688245000639 DNA binding site 688245000640 NodT family; Region: outer_NodT; TIGR01845 688245000641 Outer membrane efflux protein; Region: OEP; pfam02321 688245000642 Predicted permease; Region: FtsX; cl11418 688245000643 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 688245000644 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 688245000645 Walker A/P-loop; other site 688245000646 ATP binding site; other site 688245000647 Q-loop/lid; other site 688245000648 ABC transporter signature motif; other site 688245000649 Walker B; other site 688245000650 D-loop; other site 688245000651 H-loop/switch region; other site 688245000652 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245000653 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; cl11391 688245000654 Esterase/lipase [General function prediction only]; Region: COG1647 688245000655 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 688245000656 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 688245000657 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 688245000658 pyridoxal 5'-phosphate binding pocket; other site 688245000659 catalytic residue; other site 688245000660 Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [Energy production and conversion]; Region: SdhA; COG1053 688245000661 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245000662 domain; Region: Succ_DH_flav_C; pfam02910 688245000663 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 688245000664 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 688245000665 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 688245000666 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 688245000667 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; cl12011 688245000668 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 688245000669 S-adenosylmethionine binding site; other site 688245000670 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 688245000671 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 688245000672 inhibitor-cofactor binding pocket; inhibition site 688245000673 pyridoxal 5'-phosphate binding site; other site 688245000674 catalytic residue; other site 688245000675 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 688245000676 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 688245000677 ATP binding site; other site 688245000678 putative Mg++ binding site; other site 688245000679 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 688245000680 nucleotide binding region; other site 688245000681 ATP-binding site; other site 688245000682 RQC domain; Region: RQC; pfam09382 688245000683 HRDC domain; Region: HRDC; cl02578 688245000684 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 688245000685 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000686 DNA binding site 688245000687 UTRA domain; Region: UTRA; cl06649 688245000688 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245000689 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245000690 active site 688245000691 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245000692 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245000693 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000694 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 688245000695 dimerization interface; other site 688245000696 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl02184 688245000697 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 688245000698 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...; Region: TM_PBP2; cd06261 688245000699 dimer interface; other site 688245000700 conserved gate region; other site 688245000701 ABC-ATPase subunit interface; other site 688245000702 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245000703 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245000704 Walker A/P-loop; other site 688245000705 ATP binding site; other site 688245000706 Q-loop/lid; other site 688245000707 ABC transporter signature motif; other site 688245000708 Walker B; other site 688245000709 D-loop; other site 688245000710 H-loop/switch region; other site 688245000711 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 688245000712 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000713 DNA binding site 688245000714 UTRA domain; Region: UTRA; cl06649 688245000715 tyrosine 2,3-aminomutase; Region: Tyr_2_3_mutase; TIGR03832 688245000716 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 688245000717 active sites 688245000718 tetramer interface; other site 688245000719 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 688245000720 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000721 DNA binding site 688245000722 UTRA domain; Region: UTRA; cl06649 688245000723 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 688245000724 Sodium:solute symporter family; Region: SSF; cl00456 688245000725 urocanate hydratase; Provisional; Region: PRK05414 688245000726 urocanate hydratase; Region: hutU; TIGR01228 688245000727 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245000728 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245000729 HutD; Region: HutD; cl01532 688245000730 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 688245000731 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria...; Region: Imidazolone-5PH; cd01296 688245000732 active site 688245000733 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 688245000734 FAD binding domain; Region: FAD_binding_4; pfam01565 688245000735 histidinol-phosphate aminotransferase; Provisional; Region: PRK05166 688245000736 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 688245000737 pyridoxal 5'-phosphate binding site; other site 688245000738 homodimer interface; other site 688245000739 catalytic residue; other site 688245000740 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 688245000741 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 688245000742 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_E; cd01313 688245000743 active site 688245000744 N-formylglutamate amidohydrolase; Region: FGase; cl01522 688245000745 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 688245000746 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245000747 DNA binding residues 688245000748 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245000749 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 688245000750 NodT family; Region: outer_NodT; TIGR01845 688245000751 Outer membrane efflux protein; Region: OEP; pfam02321 688245000752 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245000753 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 688245000754 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 688245000755 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...; Region: gram_neg_porins; cd00342 688245000756 trimer interface; other site 688245000757 eyelet of channel; other site 688245000758 biotin synthetase; Region: bioB; TIGR00433 688245000759 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 688245000760 FeS/SAM binding site; other site 688245000761 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 688245000762 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 688245000763 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 688245000764 inhibitor-cofactor binding pocket; inhibition site 688245000765 pyridoxal 5'-phosphate binding site; other site 688245000766 catalytic residue; other site 688245000767 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 688245000768 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245000769 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 688245000770 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 688245000771 pyridoxal 5'-phosphate binding pocket; other site 688245000772 catalytic residue; other site 688245000773 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 688245000774 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000775 DNA binding site 688245000776 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 688245000777 pyridoxal 5'-phosphate binding site; other site 688245000778 homodimer interface; other site 688245000779 catalytic residue; other site 688245000780 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 688245000781 Permease family; Region: Xan_ur_permease; cl00967 688245000782 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 688245000783 pyridoxal 5'-phosphate (PLP) binding site; other site 688245000784 catalytic residue; other site 688245000785 acetylornithine aminotransferase; Provisional; Region: PRK02627 688245000786 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 688245000787 inhibitor-cofactor binding pocket; inhibition site 688245000788 pyridoxal 5'-phosphate binding site; other site 688245000789 catalytic residue; other site 688245000790 alanine racemase; Reviewed; Region: dadX; PRK03646 688245000791 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 688245000792 active site 688245000793 pyridoxal 5'-phosphate (PLP) binding site; other site 688245000794 substrate binding site; other site 688245000795 catalytic residues; other site 688245000796 dimer interface; other site 688245000797 lysophospholipid transporter LplT; Provisional; Region: PRK11195 688245000798 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 688245000799 putative substrate translocation pore; other site 688245000800 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 688245000801 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 688245000802 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245000803 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cd00216 688245000804 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 688245000805 Trp docking motif; other site 688245000806 'Velcro' closure; other site 688245000807 active site 688245000808 Cytochrome c; Region: Cytochrom_C; cl11414 688245000809 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 688245000810 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 688245000811 NAD binding site; other site 688245000812 catalytic residues; other site 688245000813 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; cl00174 688245000814 putative RNA binding sites; other site 688245000815 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 688245000816 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 alpha-; Region: HCP_like; cl14655 688245000817 Cysteine-rich domain; Region: CCG; pfam02754 688245000818 Cysteine-rich domain; Region: CCG; pfam02754 688245000819 FAD binding domain; Region: FAD_binding_4; pfam01565 688245000820 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 688245000821 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 688245000822 Nitrogen regulatory protein P-II; Region: P-II; cl00412 688245000823 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 688245000824 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 688245000825 Sulfatase; Region: Sulfatase; cl10460 688245000826 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 688245000827 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 688245000828 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245000829 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000830 Mg chelatase-related protein; Region: TIGR00368 688245000831 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245000832 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245000833 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000834 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 688245000835 dimerization interface; other site 688245000836 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 688245000837 putative substrate translocation pore; other site 688245000838 2-nitropropane dioxygenase; Region: NPD; pfam03060 688245000839 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...; Region: NPD_like; cd04730 688245000840 FMN binding site; other site 688245000841 substrate binding site; other site 688245000842 putative catalytic residue; other site 688245000843 feruloyl-CoA synthase; Reviewed; Region: PRK08180 688245000844 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245000845 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000846 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245000847 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245000848 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 688245000849 putative ligand binding site; other site 688245000850 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245000851 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245000852 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 688245000853 ligand binding site; other site 688245000854 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245000855 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000856 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 688245000857 putative dimerization interface; other site 688245000858 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 688245000859 Uncharacterized conserved protein [Function unknown]; Region: COG3777 688245000860 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 688245000861 active site 2 688245000862 active site 1 688245000863 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245000864 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245000865 active site 688245000866 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245000867 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 688245000868 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 688245000869 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245000870 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000871 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 688245000872 NAD(P) binding site; other site 688245000873 active site 688245000874 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 688245000875 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245000876 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245000877 Walker A/P-loop; other site 688245000878 ATP binding site; other site 688245000879 Q-loop/lid; other site 688245000880 ABC transporter signature motif; other site 688245000881 Walker B; other site 688245000882 D-loop; other site 688245000883 H-loop/switch region; other site 688245000884 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245000885 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245000886 Walker A/P-loop; other site 688245000887 ATP binding site; other site 688245000888 Q-loop/lid; other site 688245000889 ABC transporter signature motif; other site 688245000890 Walker B; other site 688245000891 D-loop; other site 688245000892 H-loop/switch region; other site 688245000893 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 688245000894 TM-ABC transporter signature motif; other site 688245000895 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 688245000896 TM-ABC transporter signature motif; other site 688245000897 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245000898 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 688245000899 putative ligand binding site; other site 688245000900 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245000901 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 688245000902 FAD binding pocket; other site 688245000903 FAD binding motif; other site 688245000904 phosphate binding motif; other site 688245000905 beta-alpha-beta structure motif; other site 688245000906 NAD binding pocket; other site 688245000907 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 688245000908 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 688245000909 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 688245000910 galactarate dehydratase; Region: galactar-dH20; TIGR03248 688245000911 SAF domain; Region: SAF; cl00555 688245000912 SAF domain; Region: SAF; cl00555 688245000913 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 688245000914 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 688245000915 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...; Region: D-glucarate_dehydratase; cd03323 688245000916 active site 688245000917 tetramer interface; other site 688245000918 Transcriptional regulators [Transcription]; Region: FadR; COG2186 688245000919 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245000920 DNA binding site 688245000921 FCD domain; Region: FCD; cl11656 688245000922 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 688245000923 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 688245000924 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in...; Region: KDGDH; cd00951 688245000925 putative active site; other site 688245000926 catalytic residue; other site 688245000927 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 688245000928 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 688245000929 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000930 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 688245000931 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...; Region: D-glucarate_dehydratase; cd03323 688245000932 active site 688245000933 tetramer interface; other site 688245000934 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 688245000935 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 688245000936 NAD(P) binding site; other site 688245000937 catalytic residues; other site 688245000938 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000939 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245000940 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 688245000941 putative effector binding pocket; other site 688245000942 dimerization interface; other site 688245000943 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 688245000944 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 688245000945 Putative cyclase; Region: Cyclase; cl00814 688245000946 LrgB-like family; Region: LrgB; cl00596 688245000947 LrgA family; Region: LrgA; cl00608 688245000948 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 688245000949 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000950 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 688245000951 dimerization interface; other site 688245000952 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 688245000953 pseudouridine synthase; Region: TIGR00093 688245000954 active site 688245000955 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245000956 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 688245000957 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 688245000958 NAD(P) transhydrogenase beta subunit; Region: PNTB; cl00566 688245000959 LysE type translocator; Region: LysE; cl00565 688245000960 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245000961 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245000962 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 688245000963 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 688245000964 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245000965 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 688245000966 HPP family; Region: HPP; pfam04982 688245000967 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-...; Region: CBS_pair; cl10010 688245000968 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 688245000969 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 688245000970 putative FMN binding site; other site 688245000971 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 688245000972 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245000973 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 688245000974 L-serine binding site; other site 688245000975 ACT domain interface; other site 688245000976 Predicted membrane protein [Function unknown]; Region: COG1297; cl14607 688245000977 putative oligopeptide transporter, OPT family; Region: TIGR00733 688245000978 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 688245000979 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 688245000980 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; cl12031 688245000981 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 688245000982 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 688245000983 GatB domain; Region: GatB_Yqey; cl11497 688245000984 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; cl11426 688245000985 Amidase; Region: Amidase; pfam01425 688245000986 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 688245000987 rod shape-determining protein MreB; Provisional; Region: PRK13927 688245000988 Cell division protein FtsA; Region: FtsA; cl11496 688245000989 rod shape-determining protein MreC; Provisional; Region: PRK13922 688245000990 rod shape-determining protein MreC; Region: MreC; pfam04085 688245000991 rod shape-determining protein MreD; Region: MreD; cl01087 688245000992 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 688245000993 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 688245000994 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245000995 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 688245000996 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 688245000997 choline dehydrogenase; Validated; Region: PRK02106 688245000998 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 688245000999 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 688245001000 Domain of unknown function DUF140; Region: DUF140; cl00510 688245001001 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 688245001002 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001003 Walker A/P-loop; other site 688245001004 ATP binding site; other site 688245001005 Q-loop/lid; other site 688245001006 ABC transporter signature motif; other site 688245001007 Walker B; other site 688245001008 D-loop; other site 688245001009 H-loop/switch region; other site 688245001010 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 688245001011 mce related protein; Region: MCE; cl03606 688245001012 cation-binding hemerythrin HHE family protein; Provisional; Region: PRK01917 688245001013 MarC family integral membrane protein; Region: MarC; cl00919 688245001014 Dienelactone hydrolase family; Region: DLH; pfam01738 688245001015 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 688245001016 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 688245001017 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 688245001018 dimer interface; other site 688245001019 allosteric magnesium binding site; other site 688245001020 active site 688245001021 aspartate-rich active site metal binding site; other site 688245001022 Schiff base residues; other site 688245001023 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 688245001024 VanZ like family; Region: VanZ; cl01971 688245001025 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 688245001026 dimer interface; other site 688245001027 [2Fe-2S] cluster binding site; other site 688245001028 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 688245001029 potential frameshift: common BLAST hit: gi|160895834|ref|YP_001561416.1| Serine-type D-Ala-D-Ala carboxypeptidase 688245001030 Beta-lactamase; Region: Beta-lactamase; cl01009 688245001031 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 688245001032 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 688245001033 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 688245001034 streptomycin interaction site; other site 688245001035 23S rRNA interaction site; other site 688245001036 aminoacyl-tRNA interaction site (A-site); other site 688245001037 16S rRNA interaction site; other site 688245001038 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 688245001039 elongation factor G; Reviewed; Region: PRK00007 688245001040 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 688245001041 G1 box; other site 688245001042 putative GEF interaction site; other site 688245001043 GTP/Mg2+ binding site; other site 688245001044 Switch I region; other site 688245001045 G2 box; other site 688245001046 G3 box; other site 688245001047 Switch II region; other site 688245001048 G4 box; other site 688245001049 G5 box; other site 688245001050 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...; Region: EFG_mtEFG_II; cd04088 688245001051 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...; Region: EFG_mtEFG1_IV; cd01434 688245001052 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...; Region: EFG_mtEFG_C; cd03713 688245001053 elongation factor Tu; Reviewed; Region: PRK00049 688245001054 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 688245001055 G1 box; other site 688245001056 GEF interaction site; other site 688245001057 GTP/Mg2+ binding site; other site 688245001058 Switch I region; other site 688245001059 G2 box; other site 688245001060 G3 box; other site 688245001061 Switch II region; other site 688245001062 G4 box; other site 688245001063 G5 box; other site 688245001064 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 688245001065 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 688245001066 Antibiotic Binding Site; other site 688245001067 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 688245001068 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 688245001069 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 688245001070 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 688245001071 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 688245001072 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 688245001073 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 688245001074 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 688245001075 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 688245001076 putative translocon binding site; other site 688245001077 protein-rRNA interface; other site 688245001078 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 688245001079 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...; Region: 30S_S3_KH; cd02412 688245001080 G-X-X-G motif; other site 688245001081 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 688245001082 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 688245001083 23S rRNA interface; other site 688245001084 5S rRNA interface; other site 688245001085 putative antibiotic binding site; other site 688245001086 L25 interface; other site 688245001087 L27 interface; other site 688245001088 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...; Region: Ribosomal_L29_HIP; cd00427 688245001089 23S rRNA interface; other site 688245001090 putative translocon interaction site; other site 688245001091 signal recognition particle (SRP54) interaction site; other site 688245001092 L23 interface; other site 688245001093 trigger factor interaction site; other site 688245001094 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 688245001095 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 688245001096 catalytic triad; other site 688245001097 dimer interface; other site 688245001098 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245001099 Coenzyme A binding pocket; other site 688245001100 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 688245001101 Cytochrome C'; Region: Cytochrom_C_2; cl01610 688245001102 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...; Region: TlpA_like_family; cd02966 688245001103 catalytic residues; other site 688245001104 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...; Region: PTS_IIA_man; cl00025 688245001105 active pocket/dimerization site; other site 688245001106 active site 688245001107 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 688245001108 regulatory protein interface; other site 688245001109 active site 688245001110 regulatory phosphorylation site; other site 688245001111 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 688245001112 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 688245001113 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 688245001114 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245001115 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 688245001116 lipoyl synthase; Provisional; Region: PRK05481 688245001117 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 688245001118 FeS/SAM binding site; other site 688245001119 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 688245001120 Protein of unknown function (DUF493); Region: DUF493; cl01102 688245001121 ATP synthase A chain; Region: ATP-synt_A; cl00413 688245001122 ATP synthase subunit C; Region: ATP-synt_C; cl00466 688245001123 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 688245001124 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 688245001125 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 688245001126 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 688245001127 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 688245001128 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 688245001129 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 688245001130 beta subunit interaction interface; other site 688245001131 Walker A motif; other site 688245001132 ATP binding site; other site 688245001133 Walker B motif; other site 688245001134 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 688245001135 ATP synthase; Region: ATP-synt; cl00365 688245001136 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 688245001137 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 688245001138 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 688245001139 alpha subunit interaction interface; other site 688245001140 Walker A motif; other site 688245001141 ATP binding site; other site 688245001142 Walker B motif; other site 688245001143 inhibitor binding site; inhibition site 688245001144 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 688245001145 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 688245001146 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 688245001147 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 protein...; Region: CSP_CDS; cd04458 688245001148 DNA binding site 688245001149 RNA-binding motif; other site 688245001150 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 688245001151 Domain of unknown function (DUF477); Region: DUF477; cl01535 688245001152 Domain of unknown function (DUF477); Region: DUF477; cl01535 688245001153 LemA family; Region: LemA; cl00742 688245001154 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245001155 NAD(P) binding site; other site 688245001156 active site 688245001157 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 688245001158 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 688245001159 Cytochrome c; Region: Cytochrom_C; cl11414 688245001160 Cytochrome c; Region: Cytochrom_C; cl11414 688245001161 NodT family; Region: outer_NodT; TIGR01845 688245001162 Outer membrane efflux protein; Region: OEP; pfam02321 688245001163 Outer membrane efflux protein; Region: OEP; pfam02321 688245001164 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 688245001165 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 688245001166 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 688245001167 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245001168 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 688245001169 elongation factor Tu; Reviewed; Region: PRK00049 688245001170 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 688245001171 G1 box; other site 688245001172 GEF interaction site; other site 688245001173 GTP/Mg2+ binding site; other site 688245001174 Switch I region; other site 688245001175 G2 box; other site 688245001176 G3 box; other site 688245001177 Switch II region; other site 688245001178 G4 box; other site 688245001179 G5 box; other site 688245001180 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 688245001181 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 688245001182 Antibiotic Binding Site; other site 688245001183 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 688245001184 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 688245001185 Transcription termination factor nusG; Region: NusG; cl02766 688245001186 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 688245001187 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 688245001188 23S rRNA interface; other site 688245001189 L7/L12 interface; other site 688245001190 putative thiostrepton binding site; other site 688245001191 L25 interface; other site 688245001192 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...; Region: Ribosomal_L1; cd00403 688245001193 mRNA/rRNA interface; other site 688245001194 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...; Region: Ribosomal_L10; cd05797 688245001195 23S rRNA interface; other site 688245001196 Interface with L7/L12 ribosomal proteins; other site 688245001197 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 688245001198 peripheral dimer interface; other site 688245001199 core dimer interface; other site 688245001200 L10 interface; other site 688245001201 L11 interface; other site 688245001202 putative EF-Tu interaction site; other site 688245001203 putative EF-G interaction site; other site 688245001204 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; cl04593 688245001205 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 688245001206 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 688245001207 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; cl04593 688245001208 RPB11 interaction site; other site 688245001209 RPB12 interaction site; other site 688245001210 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 688245001211 RPB3 interaction site; other site 688245001212 RPB1 interaction site; other site 688245001213 RPB11 interaction site; other site 688245001214 RPB10 interaction site; other site 688245001215 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 688245001216 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 688245001217 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 688245001218 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 688245001219 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 688245001220 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 688245001221 Rpb1 - Rpb6 interaction site; other site 688245001222 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 688245001223 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 688245001224 DNA binding site 688245001225 Rpb1 (beta') - Rpb2 (beta) interaction site; other site 688245001226 16S rRNA methyltransferase B; Provisional; Region: PRK10901 688245001227 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 rRNA-...; Region: NusB_Sun; cl00223 688245001228 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 688245001229 S-adenosylmethionine binding site; other site 688245001230 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 688245001231 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245001232 dimerization interface; other site 688245001233 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 688245001234 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 trans...; Region: HisKA; cd00082 688245001235 dimer interface; other site 688245001236 phosphorylation site 688245001237 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 688245001238 ATP binding site; other site 688245001239 Mg2+ binding site; other site 688245001240 G-X-G motif; other site 688245001241 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 688245001242 active site 688245001243 phosphorylation site 688245001244 intermolecular recognition site; other site 688245001245 dimerization interface; other site 688245001246 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 688245001247 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 688245001248 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 688245001249 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 688245001250 UvrD/REP helicase; Region: UvrD-helicase; cl14126 688245001251 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 688245001252 Putative ATPase (DUF699); Region: DUF699; pfam05127 688245001253 UvrD/REP helicase; Region: UvrD-helicase; cl14126 688245001254 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 688245001255 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245001256 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 688245001257 C-terminal domain interface; other site 688245001258 GSH binding site (G-site); other site 688245001259 dimer interface; other site 688245001260 Glutathione S-transferase (GST) family, C-terminal alpha helical 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...; Region: GST_C_family; cd00299 688245001261 N-terminal domain interface; other site 688245001262 dimer interface; other site 688245001263 substrate binding pocket (H-site); other site 688245001264 Protein of unknown function (DUF461); Region: DUF461; cl01071 688245001265 FIST N domain; Region: FIST; pfam08495 688245001266 FIST C domain; Region: FIST_C; pfam10442 688245001267 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245001268 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 688245001269 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245001270 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 688245001271 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 688245001272 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245001273 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 688245001274 putative substrate translocation pore; other site 688245001275 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 688245001276 putative acyl-acceptor binding pocket; other site 688245001277 Protein of unknown function (DUF3047); Region: DUF3047; pfam11249 688245001278 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 688245001279 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 688245001280 MASE1; Region: MASE1; cl01367 688245001281 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245001282 metal-binding site 688245001283 active site 688245001284 I-site; other site 688245001285 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 688245001286 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 688245001287 Ligand Binding Site; other site 688245001288 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245001289 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001290 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 688245001291 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245001292 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 688245001293 active site 688245001294 FMN binding site; other site 688245001295 substrate binding site; other site 688245001296 homotetramer interface; other site 688245001297 catalytic residue; other site 688245001298 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245001299 classical (c) SDRs; Region: SDR_c; cd05233 688245001300 NAD(P) binding site; other site 688245001301 active site 688245001302 enoyl-CoA hydratase; Provisional; Region: PRK08258 688245001303 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 688245001304 substrate binding site; other site 688245001305 oxyanion hole (OAH) forming residues; other site 688245001306 trimer interface; other site 688245001307 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245001308 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245001309 active site 688245001310 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 688245001311 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245001312 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...; Region: 4HBT; cd00586 688245001313 active site 688245001314 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 688245001315 homotrimer interaction site; other site 688245001316 putative active site; other site 688245001317 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; cl01053 688245001318 active site 688245001319 catalytic triad; other site 688245001320 oxyanion hole; other site 688245001321 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 Gram...; Region: OMPLA; cd00541 688245001322 substrate binding site; other site 688245001323 dimerization interface; other site 688245001324 active site 688245001325 calcium binding site; other site 688245001326 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 688245001327 UvrD/REP helicase; Region: UvrD-helicase; cl14126 688245001328 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cd00882 688245001329 G1 box; other site 688245001330 GTP/Mg2+ binding site; other site 688245001331 G2 box; other site 688245001332 Switch I region; other site 688245001333 G3 box; other site 688245001334 Switch II region; other site 688245001335 Membrane transport protein; Region: Mem_trans; cl09117 688245001336 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cd00411 688245001337 tetramer interface; other site 688245001338 active site/substrate binding site 688245001339 primosome assembly protein PriA; Validated; Region: PRK05580 688245001340 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 688245001341 ATP binding site; other site 688245001342 putative Mg++ binding site; other site 688245001343 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; cl12029 688245001344 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...; Region: URO-D; cd00717 688245001345 substrate binding site; other site 688245001346 active site 688245001347 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl00357 688245001348 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 688245001349 Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4233 688245001350 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 688245001351 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 688245001352 DsbD alpha interface; other site 688245001353 catalytic residues; other site 688245001354 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 688245001355 MatE; Region: MatE; pfam01554 688245001356 MatE; Region: MatE; pfam01554 688245001357 Creatinine amidohydrolase; Region: Creatininase; cl00618 688245001358 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 688245001359 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 688245001360 catalytic core; other site 688245001361 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 688245001362 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 688245001363 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...; Region: TM_PBP2; cd06261 688245001364 dimer interface; other site 688245001365 conserved gate region; other site 688245001366 putative PBP binding loops; other site 688245001367 ABC-ATPase subunit interface; other site 688245001368 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...; Region: TM_PBP2; cd06261 688245001369 dimer interface; other site 688245001370 conserved gate region; other site 688245001371 putative PBP binding loops; other site 688245001372 ABC-ATPase subunit interface; other site 688245001373 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 688245001374 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001375 Walker A/P-loop; other site 688245001376 ATP binding site; other site 688245001377 Q-loop/lid; other site 688245001378 ABC transporter signature motif; other site 688245001379 Walker B; other site 688245001380 D-loop; other site 688245001381 H-loop/switch region; other site 688245001382 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 688245001383 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 688245001384 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 688245001385 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 688245001386 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 688245001387 pyridoxal 5'-phosphate binding site; other site 688245001388 homodimer interface; other site 688245001389 catalytic residue; other site 688245001390 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 688245001391 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245001392 DNA binding site 688245001393 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 688245001394 pyridoxal 5'-phosphate binding site; other site 688245001395 homodimer interface; other site 688245001396 catalytic residue; other site 688245001397 YdjC-like protein; Region: YdjC; cl01344 688245001398 GtrA-like protein; Region: GtrA; cl00971 688245001399 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 688245001400 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 688245001401 Ligand binding site; other site 688245001402 Putative Catalytic site; other site 688245001403 DXD motif; other site 688245001404 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 688245001405 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 688245001406 SAF domain; Region: SAF; cl00555 688245001407 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 688245001408 flagellar basal body rod protein FlgB; Provisional; Region: flgB; cl09471 688245001409 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 688245001410 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 688245001411 Flagellar hook capping protein; Region: FlgD; cl04347 688245001412 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 688245001413 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 688245001414 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 688245001415 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 688245001416 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 688245001417 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 688245001418 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 688245001419 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 688245001420 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 688245001421 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 688245001422 Flagellar L-ring protein; Region: FlgH; cl00905 688245001423 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 688245001424 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 688245001425 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 688245001426 Rod binding protein; Region: Rod-binding; cl01626 688245001427 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 688245001428 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 688245001429 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 688245001430 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 688245001431 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 688245001432 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 688245001433 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 688245001434 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245001435 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 688245001436 FlhB HrpN YscU SpaS Family; Region: Bac_export_2; pfam01312 688245001437 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 688245001438 FHIPEP family; Region: FHIPEP; cl07980 688245001439 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 688245001440 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 688245001441 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245001442 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 688245001443 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...; Region: Sigma70_r4; cd06171 688245001444 DNA binding residues 688245001445 Flagellar protein FliT; Region: FliT; cl05125 688245001446 Flagellar protein FliS; Region: FliS; cl00654 688245001447 flagellar capping protein; Reviewed; Region: fliD; PRK08032 688245001448 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 688245001449 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 688245001450 flagellin; Reviewed; Region: PRK08869 688245001451 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 688245001452 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 688245001453 flagellin; Reviewed; Region: PRK08869 688245001454 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 688245001455 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 688245001456 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 688245001457 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 688245001458 flagellar motor protein MotB; Validated; Region: motB; PRK09041 688245001459 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 688245001460 ligand binding site; other site 688245001461 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 688245001462 active site 688245001463 phosphorylation site 688245001464 intermolecular recognition site; other site 688245001465 dimerization interface; other site 688245001466 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 688245001467 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 688245001468 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 688245001469 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 688245001470 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 688245001471 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 688245001472 FliG C-terminal domain; Region: FliG_C; pfam01706 688245001473 Flagellar assembly protein FliH; Region: FliH; pfam02108 688245001474 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 688245001475 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 688245001476 Walker A motif/ATP binding site; other site 688245001477 Walker B motif; other site 688245001478 Flagellar FliJ protein; Region: FliJ; cl09161 688245001479 Flagellar hook-length control protein FliK; Region: Flg_hook; cl14669 688245001480 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 688245001481 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 688245001482 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 688245001483 flagellar motor switch protein; Validated; Region: fliN; PRK05698 688245001484 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 688245001485 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 688245001486 FliP family; Region: FliP; cl00593 688245001487 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 688245001488 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 688245001489 response regulator; Provisional; Region: PRK09483 688245001490 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 688245001491 active site 688245001492 phosphorylation site 688245001493 intermolecular recognition site; other site 688245001494 dimerization interface; other site 688245001495 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...; Region: LuxR_C_like; cd06170 688245001496 DNA binding residues 688245001497 dimerization interface; other site 688245001498 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 688245001499 active site 688245001500 phosphorylation site 688245001501 intermolecular recognition site; other site 688245001502 dimerization interface; other site 688245001503 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 688245001504 Histidine kinase; Region: HisKA_3; pfam07730 688245001505 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 688245001506 ATP binding site; other site 688245001507 Mg2+ binding site; other site 688245001508 G-X-G motif; other site 688245001509 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 688245001510 active site 688245001511 phosphorylation site 688245001512 intermolecular recognition site; other site 688245001513 dimerization interface; other site 688245001514 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 688245001515 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 688245001516 putative binding surface; other site 688245001517 active site 688245001518 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 688245001519 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 688245001520 ATP binding site; other site 688245001521 Mg2+ binding site; other site 688245001522 G-X-G motif; other site 688245001523 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 688245001524 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 688245001525 putative CheA interaction surface; other site 688245001526 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 688245001527 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 688245001528 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; cl12011 688245001529 CheD; Region: CheD; cl00810 688245001530 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 688245001531 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 688245001532 active site 688245001533 phosphorylation site 688245001534 intermolecular recognition site; other site 688245001535 dimerization interface; other site 688245001536 CheB methylesterase; Region: CheB_methylest; pfam01339 688245001537 ABC transporter ATPase component; Reviewed; Region: PRK11147 688245001538 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001539 Walker A/P-loop; other site 688245001540 ATP binding site; other site 688245001541 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001542 Q-loop/lid; other site 688245001543 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245001544 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245001545 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245001546 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 688245001547 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 688245001548 DNA binding residues 688245001549 putative dimer interface; other site 688245001550 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 688245001551 CoenzymeA binding site; other site 688245001552 subunit interaction site; other site 688245001553 PHB binding site; other site 688245001554 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 688245001555 isovaleryl-CoA dehydrogenase; Region: PLN02519 688245001556 substrate binding site; other site 688245001557 FAD binding site; other site 688245001558 catalytic base; other site 688245001559 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 688245001560 active site clefts 688245001561 zinc binding site; other site 688245001562 dimer interface; other site 688245001563 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 688245001564 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 688245001565 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 688245001566 dimer interface; other site 688245001567 active site 688245001568 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 688245001569 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245001570 NAD(P) binding site; other site 688245001571 active site 688245001572 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245001573 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245001574 active site 688245001575 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 688245001576 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; cl12031 688245001577 Protein of unknown function (DUF421); Region: DUF421; cl00990 688245001578 SEC-C motif; Region: SEC-C; cl12132 688245001579 hypothetical protein; Provisional; Region: PRK04233 688245001580 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 688245001581 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 688245001582 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 trans-...; Region: HisKA; cd00082 688245001583 dimer interface; other site 688245001584 phosphorylation site 688245001585 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 688245001586 ATP binding site; other site 688245001587 Mg2+ binding site; other site 688245001588 G-X-G motif; other site 688245001589 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 688245001590 active site 688245001591 phosphorylation site 688245001592 intermolecular recognition site; other site 688245001593 dimerization interface; other site 688245001594 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245001595 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 688245001596 active site 688245001597 phosphorylation site 688245001598 intermolecular recognition site; other site 688245001599 dimerization interface; other site 688245001600 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...; Region: LuxR_C_like; cd06170 688245001601 DNA binding residues 688245001602 dimerization interface; other site 688245001603 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; cl11391 688245001604 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 688245001605 DNA-binding transcriptional regulator AraC; Provisional; Region: PRK10572 688245001606 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245001607 AMP-binding domain protein; Validated; Region: PRK08315 688245001608 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245001609 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 688245001610 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 688245001611 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245001612 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 688245001613 enoyl-CoA hydratase; Provisional; Region: PRK06688 688245001614 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 688245001615 substrate binding site; other site 688245001616 oxyanion hole (OAH) forming residues; other site 688245001617 trimer interface; other site 688245001618 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 688245001619 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245001620 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245001621 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245001622 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 688245001623 carboxyltransferase (CT) interaction site; other site 688245001624 biotinylation site; other site 688245001625 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245001626 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 688245001627 active site 688245001628 catalytic residues; other site 688245001629 metal-binding site 688245001630 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 688245001631 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 688245001632 putative deacylase active site; other site 688245001633 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 688245001634 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 688245001635 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 1,2...; Region: DsbA_HCCA_Iso; cd03022 688245001636 putative catalytic residue; other site 688245001637 Phosphoesterase family; Region: Phosphoesterase; cl10627 688245001638 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 688245001639 Sodium:solute symporter family; Region: SSF; cl00456 688245001640 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 688245001641 Protein of unknown function, DUF485; Region: DUF485; cl01231 688245001642 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 688245001643 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 688245001644 putative substrate translocation pore; other site 688245001645 metabolite-proton symporter; Region: 2A0106; TIGR00883 688245001646 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...; Region: gram_neg_porins; cd00342 688245001647 trimer interface; other site 688245001648 eyelet of channel; other site 688245001649 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 688245001650 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245001651 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245001652 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001653 Walker A/P-loop; other site 688245001654 ATP binding site; other site 688245001655 Q-loop/lid; other site 688245001656 ABC transporter signature motif; other site 688245001657 Walker B; other site 688245001658 D-loop; other site 688245001659 H-loop/switch region; other site 688245001660 excinuclease ABC, A subunit; Region: uvra; TIGR00630 688245001661 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245001662 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 688245001663 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245001664 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 688245001665 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; cl09110 688245001666 DctM-like transporters; Region: DctM; pfam06808 688245001667 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245001668 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245001669 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 688245001670 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 688245001671 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 688245001672 G1 box; other site 688245001673 putative GEF interaction site; other site 688245001674 GTP/Mg2+ binding site; other site 688245001675 Switch I region; other site 688245001676 G2 box; other site 688245001677 G3 box; other site 688245001678 Switch II region; other site 688245001679 G4 box; other site 688245001680 G5 box; other site 688245001681 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...; Region: Translation_Factor_II_like; cl02787 688245001682 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 688245001683 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245001684 putative substrate translocation pore; other site 688245001685 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 688245001686 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 688245001687 K+-transporting ATPase, c chain; Region: KdpC; cl00944 688245001688 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 688245001689 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245001690 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 688245001691 sensor protein KdpD; Provisional; Region: PRK10490 688245001692 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 688245001693 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 688245001694 Ligand Binding Site; other site 688245001695 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 trans-...; Region: HisKA; cd00082 688245001696 dimer interface; other site 688245001697 phosphorylation site 688245001698 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 688245001699 ATP binding site; other site 688245001700 Mg2+ binding site; other site 688245001701 G-X-G motif; other site 688245001702 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 688245001703 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 688245001704 active site 688245001705 phosphorylation site 688245001706 intermolecular recognition site; other site 688245001707 dimerization interface; other site 688245001708 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...; Region: trans_reg_C; cd00383 688245001709 DNA binding site 688245001710 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 688245001711 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; Region: AdoHcyase; cd00401 688245001712 oligomerization interface; other site 688245001713 active site 688245001714 NAD+ binding site; other site 688245001715 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; cl09940 688245001716 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; cl12011 688245001717 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; cl12011 688245001718 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...; Region: MTHFR; cd00537 688245001719 FAD binding site; other site 688245001720 rare lipoprotein A; Provisional; Region: PRK10672 688245001721 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 688245001722 Protein of unknown function (DUF519); Region: DUF519; cl04492 688245001723 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 688245001724 23S rRNA interface; other site 688245001725 L3 interface; other site 688245001726 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 688245001727 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 688245001728 putative transporter; Provisional; Region: PRK10504 688245001729 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 688245001730 putative substrate translocation pore; other site 688245001731 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 688245001732 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 688245001733 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245001734 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 688245001735 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 688245001736 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 688245001737 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245001738 Permease family; Region: Xan_ur_permease; cl00967 688245001739 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 688245001740 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...; Region: TM_PBP2; cd06261 688245001741 dimer interface; other site 688245001742 conserved gate region; other site 688245001743 putative PBP binding loops; other site 688245001744 ABC-ATPase subunit interface; other site 688245001745 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245001746 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245001747 Walker A/P-loop; other site 688245001748 ATP binding site; other site 688245001749 Q-loop/lid; other site 688245001750 ABC transporter signature motif; other site 688245001751 Walker B; other site 688245001752 D-loop; other site 688245001753 H-loop/switch region; other site 688245001754 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 688245001755 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 688245001756 active site 688245001757 non-prolyl cis peptide bond; other site 688245001758 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 688245001759 putative peptidase; Provisional; Region: PRK11649 688245001760 Peptidase family M23; Region: Peptidase_M23; pfam01551 688245001761 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 688245001762 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 688245001763 active site 688245001764 HIGH motif; other site 688245001765 dimer interface; other site 688245001766 KMSKS motif; other site 688245001767 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; cl09940 688245001768 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001769 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245001770 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 688245001771 dimerization interface; other site 688245001772 substrate binding pocket; other site 688245001773 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 688245001774 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 688245001775 Substrate binding site; other site 688245001776 Mg++ binding site; other site 688245001777 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 688245001778 active site 688245001779 substrate binding site; other site 688245001780 CoA binding site; other site 688245001781 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 trans...; Region: HisKA; cd00082 688245001782 dimer interface; other site 688245001783 phosphorylation site 688245001784 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 688245001785 ATP binding site; other site 688245001786 Mg2+ binding site; other site 688245001787 G-X-G motif; other site 688245001788 MASE2 domain; Region: MASE2; pfam05230 688245001789 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245001790 metal-binding site 688245001791 active site 688245001792 I-site; other site 688245001793 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001794 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001795 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 688245001796 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...; Region: GFAT; cd00714 688245001797 glutaminase active site; other site 688245001798 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 688245001799 dimer interface; other site 688245001800 active site 688245001801 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 688245001802 dimer interface; other site 688245001803 active site 688245001804 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; cl09110 688245001805 DctM-like transporters; Region: DctM; pfam06808 688245001806 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245001807 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245001808 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245001809 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245001810 DNA binding site 688245001811 FCD domain; Region: FCD; cl11656 688245001812 Protein of unknown function (DUF969); Region: DUF969; cl01573 688245001813 Protein of unknown function (DUF979); Region: DUF979; cl01572 688245001814 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 688245001815 putative substrate binding pocket; other site 688245001816 AC domain interface; other site 688245001817 catalytic triad; other site 688245001818 AB domain interface; other site 688245001819 interchain disulfide; other site 688245001820 LamB/YcsF family; Region: LamB_YcsF; cl00664 688245001821 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 688245001822 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 688245001823 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 688245001824 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 688245001825 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 688245001826 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245001827 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245001828 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245001829 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 688245001830 carboxyltransferase (CT) interaction site; other site 688245001831 biotinylation site; other site 688245001832 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 688245001833 metal-binding site 688245001834 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 688245001835 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 688245001836 metal-binding site 688245001837 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245001838 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; cl11391 688245001839 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 688245001840 Lumazine binding domain; Region: Lum_binding; pfam00677 688245001841 Lumazine binding domain; Region: Lum_binding; pfam00677 688245001842 Predicted acyltransferase [General function prediction only]; Region: COG4801 688245001843 Protein of unknown function (DUF342); Region: DUF342; pfam03961 688245001844 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 688245001845 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 688245001846 pyridoxal 5'-phosphate binding site; other site 688245001847 homodimer interface; other site 688245001848 catalytic residue; other site 688245001849 Protein of unknown function (DUF1338); Region: DUF1338; cl02226 688245001850 Protein of unknown function (DUF1338); Region: DUF1338; cl02226 688245001851 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001852 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245001853 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 688245001854 dimerization interface; other site 688245001855 substrate binding pocket; other site 688245001856 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...; Region: PBPb; cd00134 688245001857 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245001858 substrate binding pocket; other site 688245001859 membrane-bound complex binding site; other site 688245001860 hinge residues; other site 688245001861 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 688245001862 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 688245001863 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...; Region: gram_neg_porins; cd00342 688245001864 eyelet of channel; other site 688245001865 trimer interface; other site 688245001866 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 688245001867 DNA-K related protein; Region: DUF3731; pfam12531 688245001868 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 688245001869 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 688245001870 Nitrate and nitrite sensing; Region: NIT; pfam08376 688245001871 ANTAR domain; Region: ANTAR; pfam03861 688245001872 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 688245001873 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...; Region: TM_PBP2; cd06261 688245001874 dimer interface; other site 688245001875 conserved gate region; other site 688245001876 putative PBP binding loops; other site 688245001877 ABC-ATPase subunit interface; other site 688245001878 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245001879 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 688245001880 Walker A/P-loop; other site 688245001881 ATP binding site; other site 688245001882 Q-loop/lid; other site 688245001883 ABC transporter signature motif; other site 688245001884 Walker B; other site 688245001885 D-loop; other site 688245001886 H-loop/switch region; other site 688245001887 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 688245001888 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245001889 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 688245001890 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 688245001891 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 688245001892 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 688245001893 [2Fe-2S] cluster binding site; other site 688245001894 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 oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 688245001895 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 688245001896 [4Fe-4S] binding site; other site 688245001897 molybdopterin cofactor binding site; other site 688245001898 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 oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 688245001899 molybdopterin cofactor binding site; other site 688245001900 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 688245001901 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 688245001902 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245001903 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 688245001904 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 688245001905 tetramerization interface; other site 688245001906 NAD(P) binding site; other site 688245001907 catalytic residues; other site 688245001908 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 688245001909 N-terminal plug; other site 688245001910 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245001911 ligand-binding site; other site 688245001912 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 688245001913 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245001914 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding...; Region: HemV-2; cd01147 688245001915 putative metal binding site; other site 688245001916 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...; Region: TM_ABC_iron-siderophores_like; cd06550 688245001917 putative PBP binding regions; other site 688245001918 ABC-ATPase subunit interface; other site 688245001919 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 688245001920 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245001921 Walker A/P-loop; other site 688245001922 ATP binding site; other site 688245001923 Q-loop/lid; other site 688245001924 ABC transporter signature motif; other site 688245001925 Walker B; other site 688245001926 D-loop; other site 688245001927 H-loop/switch region; other site 688245001928 Fusaric acid resistance protein family; Region: FUSC; pfam04632 688245001929 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001930 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 688245001931 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 688245001932 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 688245001933 putative dimerization interface; other site 688245001934 CreA protein; Region: CreA; cl01154 688245001935 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245001936 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 688245001937 N-terminal plug; other site 688245001938 ligand-binding site; other site 688245001939 cyanophycin synthetase; Provisional; Region: PRK14016 688245001940 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245001941 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245001942 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245001943 cyanophycin synthetase; Provisional; Region: PRK14016 688245001944 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245001945 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 688245001946 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245001947 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 688245001948 Walker A/P-loop; other site 688245001949 ATP binding site; other site 688245001950 Q-loop/lid; other site 688245001951 ABC transporter signature motif; other site 688245001952 Walker B; other site 688245001953 D-loop; other site 688245001954 H-loop/switch region; other site 688245001955 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 688245001956 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...; Region: EFh; cd00051 688245001957 Ca2+ binding site; other site 688245001958 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 688245001959 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 688245001960 general secretion pathway protein F; Region: GspF; TIGR02120 688245001961 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245001962 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245001963 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245001964 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245001965 NAD(P) binding site; other site 688245001966 active site 688245001967 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...; Region: GST_N_GTT1_like; cd03046 688245001968 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245001969 putative C-terminal domain interface; other site 688245001970 putative GSH binding site (G-site); other site 688245001971 putative dimer interface; other site 688245001972 GST_C family, unknown subfamily 8; 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_C_8; cd03207 688245001973 putative N-terminal domain interface; other site 688245001974 putative dimer interface; other site 688245001975 putative substrate binding pocket (H-site); other site 688245001976 Predicted transcriptional regulator [Transcription]; Region: COG2378 688245001977 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245001978 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 688245001979 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 688245001980 ABC transporter C family member; Provisional; Region: PLN03232 688245001981 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 688245001982 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 688245001983 Walker A motif; other site 688245001984 ATP binding site; other site 688245001985 Walker B motif; other site 688245001986 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 688245001987 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 688245001988 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 688245001989 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 688245001990 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 688245001991 General secretion pathway protein L (GspL); Region: GspL; cl11448 688245001992 General secretion pathway protein K; Region: GspK; pfam03934 688245001993 general secretion pathway protein J; Region: gspJ; TIGR01711 688245001994 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 688245001995 general secretion pathway protein I; Region: gspI; TIGR01707 688245001996 Bacterial type II secretion system protein I/J; Region: GSPII_IJ; pfam02501 688245001997 Type II transport protein GspH; Region: GspH; pfam12019 688245001998 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 688245001999 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 688245002000 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 688245002001 threonine dehydratase; Reviewed; Region: PRK09224 688245002002 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 688245002003 tetramer interface; other site 688245002004 pyridoxal 5'-phosphate binding site; other site 688245002005 catalytic residue; other site 688245002006 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 688245002007 putative Ile/Val binding site; other site 688245002008 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 688245002009 putative Ile/Val binding site; other site 688245002010 OsmC-like protein; Region: OsmC; cl00767 688245002011 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 688245002012 diiron binding motif; other site 688245002013 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...; Region: gram_neg_porins; cd00342 688245002014 eyelet of channel; other site 688245002015 trimer interface; other site 688245002016 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...; Region: gram_neg_porins; cd00342 688245002017 trimer interface; other site 688245002018 eyelet of channel; other site 688245002019 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 688245002020 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 688245002021 ring oligomerisation interface; other site 688245002022 ATP/Mg binding site; other site 688245002023 stacking interactions; other site 688245002024 hinge regions; other site 688245002025 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...; Region: cpn10; cd00320 688245002026 oligomerisation interface; other site 688245002027 mobile loop; other site 688245002028 roof hairpin; other site 688245002029 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 688245002030 H-NS histone family; Region: Histone_HNS; pfam00816 688245002031 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245002032 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245002033 Coenzyme A binding pocket; other site 688245002034 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional; Region: PRK05379 688245002035 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245002036 active site 688245002037 nucleotide binding site; other site 688245002038 HIGH motif; other site 688245002039 KMSKS motif; other site 688245002040 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...; Region: Nudix_Hydrolase; cl00447 688245002041 nudix motif; other site 688245002042 NAD synthetase; Provisional; Region: PRK13981 688245002043 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 688245002044 multimer interface; other site 688245002045 active site 688245002046 catalytic triad; other site 688245002047 protein interface 1; other site 688245002048 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...; Region: NAD_synthase; cd00553 688245002049 homodimer interface; other site 688245002050 NAD binding pocket; other site 688245002051 ATP binding pocket; other site 688245002052 Mg binding site; other site 688245002053 active-site loop 688245002054 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 688245002055 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: PncB_like; cd01401 688245002056 active site 688245002057 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; cl00220 688245002058 catalytic triad; other site 688245002059 conserved cis-peptide bond; other site 688245002060 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...; Region: Nudix_Hydrolase; cd02883 688245002061 nudix motif; other site 688245002062 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...; Region: Nudix_Hydrolase; cl00447 688245002063 S-adenosylmethionine synthetase; Validated; Region: PRK05250 688245002064 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 688245002065 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 688245002066 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 688245002067 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 688245002068 putative acyl-acceptor binding pocket; other site 688245002069 lipid A biosynthesis lauroyl acyltransferase; Provisional; Region: PRK08734 688245002070 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 688245002071 putative acyl-acceptor binding pocket; other site 688245002072 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245002073 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; cl12031 688245002074 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 688245002075 G1 box; other site 688245002076 GTP/Mg2+ binding site; other site 688245002077 Switch I region; other site 688245002078 G2 box; other site 688245002079 G3 box; other site 688245002080 Switch II region; other site 688245002081 G4 box; other site 688245002082 G5 box; other site 688245002083 Cytochrome c; Region: Cytochrom_C; cl11414 688245002084 Cytochrome c; Region: Cytochrom_C; cl11414 688245002085 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 688245002086 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 688245002087 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 688245002088 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 688245002089 Moco binding site; other site 688245002090 metal coordination site; other site 688245002091 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 688245002092 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245002093 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cl00238 688245002094 putative iron binding site; other site 688245002095 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 688245002096 Transglycosylase; Region: Transgly; cl07896 688245002097 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245002098 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 688245002099 Cell division protein FtsA; Region: FtsA; cl11496 688245002100 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 688245002101 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 688245002102 Pilus assembly protein, PilO; Region: PilO; cl01234 688245002103 Pilus assembly protein, PilP; Region: PilP; cl01235 688245002104 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 688245002105 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 688245002106 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 688245002107 shikimate kinase; Reviewed; Region: aroK; PRK00131 688245002108 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...; Region: SK; cd00464 688245002109 ADP binding site; other site 688245002110 magnesium binding site; other site 688245002111 putative shikimate binding site; other site 688245002112 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 688245002113 active site 688245002114 dimer interface; other site 688245002115 metal-binding site 688245002116 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 688245002117 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245002118 Zn2+ binding site; other site 688245002119 Mg2+ binding site; other site 688245002120 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245002121 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 688245002122 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 688245002123 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 688245002124 active site 688245002125 dimer interface; other site 688245002126 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 688245002127 dimer interface; other site 688245002128 active site 688245002129 transaldolase-like protein; Provisional; Region: PTZ00411 688245002130 Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The...; Region: Transaldolase_TalAB; cd00957 688245002131 active site 688245002132 dimer interface; other site 688245002133 catalytic residue; other site 688245002134 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 688245002135 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 688245002136 putative active site; other site 688245002137 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245002138 classical (c) SDRs; Region: SDR_c; cd05233 688245002139 NAD(P) binding site; other site 688245002140 active site 688245002141 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 688245002142 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 688245002143 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 688245002144 dimer interface; other site 688245002145 active site 688245002146 Coenzyme A transferase; Region: CoA_trans; cl00773 688245002147 Coenzyme A transferase; Region: CoA_trans; cl00773 688245002148 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 688245002149 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002150 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245002151 Transposase IS200 like; Region: Transposase_17; cl00848 688245002152 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 688245002153 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 N-...; Region: GltS; cd00713 688245002154 active site 688245002155 dimer interface; other site 688245002156 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 688245002157 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...; Region: GltS_FMN; cd02808 688245002158 active site 688245002159 FMN binding site; other site 688245002160 substrate binding site; other site 688245002161 3Fe-4S cluster binding site; other site 688245002162 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 688245002163 domain interface; other site 688245002164 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 688245002165 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245002166 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 688245002167 TM1410 hypothetical-related protein; Region: DUF297; cl00997 688245002168 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 688245002169 Predicted integral membrane protein [Function unknown]; Region: COG5616 688245002170 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...; Region: GT1_like_3; cd03813 688245002171 Predicted membrane protein [Function unknown]; Region: COG4267 688245002172 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245002173 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...; Region: PBPb; cd00134 688245002174 substrate binding pocket; other site 688245002175 membrane-bound complex binding site; other site 688245002176 hinge residues; other site 688245002177 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 688245002178 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...; Region: TM_PBP2; cd06261 688245002179 dimer interface; other site 688245002180 conserved gate region; other site 688245002181 putative PBP binding loops; other site 688245002182 ABC-ATPase subunit interface; other site 688245002183 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 688245002184 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 688245002185 Walker A/P-loop; other site 688245002186 ATP binding site; other site 688245002187 Q-loop/lid; other site 688245002188 ABC transporter signature motif; other site 688245002189 Walker B; other site 688245002190 D-loop; other site 688245002191 H-loop/switch region; other site 688245002192 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 688245002193 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 688245002194 Walker A/P-loop; other site 688245002195 ATP binding site; other site 688245002196 Q-loop/lid; other site 688245002197 ABC transporter signature motif; other site 688245002198 Walker B; other site 688245002199 D-loop; other site 688245002200 H-loop/switch region; other site 688245002201 Domain of unknown function DUF140; Region: DUF140; cl00510 688245002202 mce related protein; Region: MCE; cl03606 688245002203 VacJ like lipoprotein; Region: VacJ; cl01073 688245002204 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 688245002205 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 688245002206 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 688245002207 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency...; Region: ABC_subfamily_A; cd03263 688245002208 Walker A/P-loop; other site 688245002209 ATP binding site; other site 688245002210 Q-loop/lid; other site 688245002211 ABC transporter signature motif; other site 688245002212 Walker B; other site 688245002213 D-loop; other site 688245002214 H-loop/switch region; other site 688245002215 ABC-2 type transporter; Region: ABC2_membrane; cl11417 688245002216 BolA-like protein; Region: BolA; cl00386 688245002217 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 688245002218 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 688245002219 hinge; other site 688245002220 active site 688245002221 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 688245002222 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 oxidation of L-histidinol to L...; Region: Histidinol_dh; cd06572 688245002223 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 688245002224 NAD binding site; other site 688245002225 dimerization interface; other site 688245002226 product binding site; other site 688245002227 substrate binding site; other site 688245002228 zinc binding site; other site 688245002229 catalytic residues; other site 688245002230 Beta-lactamase; Region: Beta-lactamase; cl01009 688245002231 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 688245002232 PIN domain; Region: PIN; cl09128 688245002233 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 688245002234 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 688245002235 pyridoxal 5'-phosphate binding site; other site 688245002236 homodimer interface; other site 688245002237 catalytic residue; other site 688245002238 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 688245002239 putative active site pocket; other site 688245002240 4-fold oligomerization interface; other site 688245002241 metal binding residues; metal-binding site 688245002242 3-fold/trimer interface; other site 688245002243 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 688245002244 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 688245002245 putative active site; other site 688245002246 oxyanion strand; other site 688245002247 catalytic triad; other site 688245002248 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 688245002249 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 688245002250 catalytic residues; other site 688245002251 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 688245002252 active site 688245002253 phosphate binding residues; other site 688245002254 catalytic residues; other site 688245002255 hypothetical protein; Provisional; Region: PRK09936 688245002256 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5298 688245002257 Uncharacterized protein conserved in bacteria (DUF2334); Region: DUF2334; pfam10096 688245002258 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 688245002259 binding surface 688245002260 TPR motif; other site 688245002261 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 688245002262 bacteriophage N4 receptor, outer membrane subunit; Provisional; Region: PRK09782 688245002263 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 688245002264 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 688245002265 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 688245002266 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 688245002267 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 688245002268 active site 688245002269 homodimer interface; other site 688245002270 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 UDP-N-...; Region: GlmM; cd05802 688245002271 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 688245002272 active site 688245002273 substrate binding site; other site 688245002274 metal-binding site 688245002275 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 688245002276 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)-formimino-5-; Region: HisF; cd04731 688245002277 substrate binding site; other site 688245002278 glutamase interaction surface; other site 688245002279 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 688245002280 Phosphoribosyl-ATP pyrophosphohydrolase; Region: PRA-PH; cl00345 688245002281 Predicted membrane protein [Function unknown]; Region: COG3671 688245002282 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 688245002283 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 688245002284 active site 688245002285 nucleophile elbow; other site 688245002286 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 688245002287 nucleotide binding site/active site; other site 688245002288 HIT family signature motif; other site 688245002289 catalytic residue; other site 688245002290 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 688245002291 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 688245002292 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 688245002293 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 688245002294 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 688245002295 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 C-...; Region: PDZ_serine_protease; cd00987 688245002296 protein binding site; other site 688245002297 metabolite-proton symporter; Region: 2A0106; TIGR00883 688245002298 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 688245002299 putative substrate translocation pore; other site 688245002300 Transcriptional regulators [Transcription]; Region: FadR; COG2186 688245002301 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245002302 DNA binding site 688245002303 FCD domain; Region: FCD; cl11656 688245002304 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 688245002305 enoyl-CoA hydratase; Provisional; Region: PRK06127 688245002306 substrate binding site; other site 688245002307 oxyanion hole (OAH) forming residues; other site 688245002308 trimer interface; other site 688245002309 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 688245002310 malonyl-CoA synthase; Validated; Region: PRK07514 688245002311 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245002312 Uncharacterized conserved protein [Function unknown]; Region: COG0327 688245002313 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl01309 688245002314 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 688245002315 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 688245002316 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 688245002317 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 688245002318 [2Fe-2S] cluster binding site; other site 688245002319 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 688245002320 Qi binding site; other site 688245002321 intrachain domain interface; other site 688245002322 interchain domain interface; other site 688245002323 cytochrome b; Provisional; Region: CYTB; MTH00145 688245002324 heme bH binding site; other site 688245002325 heme bL binding site; other site 688245002326 Qo binding site; other site 688245002327 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 688245002328 interchain domain interface; other site 688245002329 intrachain domain interface; other site 688245002330 Qi binding site; other site 688245002331 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 688245002332 Qo binding site; other site 688245002333 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 688245002334 stringent starvation protein A; Provisional; Region: sspA; PRK09481 688245002335 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 688245002336 C-terminal domain interface; other site 688245002337 putative GSH binding site (G-site); other site 688245002338 dimer interface; other site 688245002339 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_C_SspA; cd03186 688245002340 dimer interface; other site 688245002341 N-terminal domain interface; other site 688245002342 Stringent starvation protein B; Region: SspB; cl01120 688245002343 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12898 688245002344 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 688245002345 SecA Wing and Scaffold domain; Region: SecA_SW; pfam07516 688245002346 hypothetical protein; Provisional; Region: PRK10396 688245002347 SEC-C motif; Region: SEC-C; cl12132 688245002348 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...; Region: OAT; cd02152 688245002349 heterotetramer interface; other site 688245002350 active site pocket 688245002351 cleavage site 688245002352 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 688245002353 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245002354 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 688245002355 active site 688245002356 8-oxo-dGMP binding site; other site 688245002357 nudix motif; other site 688245002358 metal-binding site 688245002359 Domain of unknown function (DUF329); Region: DUF329; cl01144 688245002360 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 688245002361 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 688245002362 CoA-binding site; other site 688245002363 ATP-binding; other site 688245002364 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 688245002365 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 688245002366 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 688245002367 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 688245002368 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245002369 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245002370 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 688245002371 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 688245002372 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 688245002373 Walker A motif; other site 688245002374 ATP binding site; other site 688245002375 Walker B motif; other site 688245002376 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 688245002377 substrate binding pocket; other site 688245002378 chain length determination region; other site 688245002379 substrate-Mg2+ binding site; other site 688245002380 catalytic residues; other site 688245002381 aspartate-rich region 1; other site 688245002382 active site lid residues 688245002383 aspartate-rich region 2; other site 688245002384 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 688245002385 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 688245002386 GTPase CgtA; Reviewed; Region: obgE; PRK12299 688245002387 GTP1/OBG; Region: GTP1_OBG; pfam01018 688245002388 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 688245002389 G1 box; other site 688245002390 GTP/Mg2+ binding site; other site 688245002391 Switch I region; other site 688245002392 G2 box; other site 688245002393 G3 box; other site 688245002394 Switch II region; other site 688245002395 G4 box; other site 688245002396 G5 box; other site 688245002397 gamma-glutamyl kinase; Provisional; Region: PRK05429 688245002398 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 688245002399 nucleotide binding site; other site 688245002400 homotetrameric interface; other site 688245002401 putative phosphate binding site; other site 688245002402 putative allosteric binding site; other site 688245002403 PUA domain; Region: PUA; cl00607 688245002404 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...; Region: Ap4A_hydrolase_plant_like; cd03671 688245002405 putative active site; other site 688245002406 Ap4A binding site; other site 688245002407 nudix motif; other site 688245002408 putative metal binding site; other site 688245002409 prolyl-tRNA synthetase; Provisional; Region: PRK09194 688245002410 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 formation...; Region: ProRS_core_prok; cd00779 688245002411 dimer interface; other site 688245002412 motif 1; other site 688245002413 active site 688245002414 motif 2; other site 688245002415 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 single-...; Region: ProRS-INS; cd04334 688245002416 putative deacylase active site; other site 688245002417 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 688245002418 active site 688245002419 motif 3; other site 688245002420 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-...; Region: ProRS_anticodon_short; cd00861 688245002421 anticodon binding site; other site 688245002422 murein transglycosylase C; Provisional; Region: mltC; PRK11671 688245002423 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 catalyze...; Region: LT_GEWL; cd00254 688245002424 N-acetyl-D-glucosamine binding site; other site 688245002425 catalytic residue; other site 688245002426 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 688245002427 Domain of unknown function DUF21; Region: DUF21; pfam01595 688245002428 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 688245002429 Transporter associated domain; Region: CorC_HlyC; pfam03471 688245002430 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 688245002431 RNA/DNA hybrid binding site; other site 688245002432 active site 688245002433 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 688245002434 putative GSH binding site; other site 688245002435 catalytic residues; other site 688245002436 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 688245002437 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 688245002438 S-adenosylmethionine binding site; other site 688245002439 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 688245002440 peptide chain release factor 1; Validated; Region: prfA; PRK00591 688245002441 RF-1 domain; Region: RF-1; cl02875 688245002442 RF-1 domain; Region: RF-1; cl02875 688245002443 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 688245002444 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 688245002445 tRNA; other site 688245002446 putative tRNA binding site; other site 688245002447 putative NADP binding site; other site 688245002448 Glutamyl-tRNAGlu reductase, dimerization domain; Region: GlutR_dimer; pfam00745 688245002449 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245002450 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002451 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 688245002452 dimerization interface; other site 688245002453 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 688245002454 N-formylglutamate amidohydrolase; Region: FGase; cl01522 688245002455 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245002456 Sel1 repeat; Region: Sel1; cl02723 688245002457 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245002458 Sel1 repeat; Region: Sel1; cl02723 688245002459 Sel1 repeat; Region: Sel1; cl02723 688245002460 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245002461 Sel1 repeat; Region: Sel1; cl02723 688245002462 Sel1 repeat; Region: Sel1; cl02723 688245002463 Sel1 repeat; Region: Sel1; cl02723 688245002464 Sel1 repeat; Region: Sel1; cl02723 688245002465 Sel1 repeat; Region: Sel1; cl02723 688245002466 Sel1 repeat; Region: Sel1; cl02723 688245002467 Sel1 repeat; Region: Sel1; cl02723 688245002468 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 688245002469 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 688245002470 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 688245002471 putative active site; other site 688245002472 catalytic site; other site 688245002473 putative metal binding site; other site 688245002474 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 688245002475 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 688245002476 Walker A/P-loop; other site 688245002477 ATP binding site; other site 688245002478 Q-loop/lid; other site 688245002479 ABC transporter signature motif; other site 688245002480 Walker B; other site 688245002481 D-loop; other site 688245002482 H-loop/switch region; other site 688245002483 TOBE domain; Region: TOBE_2; cl01440 688245002484 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...; Region: TM_PBP2; cd06261 688245002485 dimer interface; other site 688245002486 conserved gate region; other site 688245002487 putative PBP binding loops; other site 688245002488 ABC-ATPase subunit interface; other site 688245002489 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...; Region: TM_PBP2; cd06261 688245002490 dimer interface; other site 688245002491 conserved gate region; other site 688245002492 ABC-ATPase subunit interface; other site 688245002493 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 688245002494 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 688245002495 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 688245002496 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 688245002497 FAD binding domain; Region: FAD_binding_4; pfam01565 688245002498 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 688245002499 Heterodisulfide reductase, subunit C [Energy production and conversion]; Region: HdrC; COG1150 688245002500 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 688245002501 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 688245002502 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 688245002503 nucleotide binding site/active site; other site 688245002504 HIT family signature motif; other site 688245002505 catalytic residue; other site 688245002506 Protein of unknown function (DUF971); Region: DUF971; cl01414 688245002507 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 688245002508 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 688245002509 S-adenosylmethionine binding site; other site 688245002510 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; cl12011 688245002511 Tim44-like domain; Region: Tim44; cl09208 688245002512 SCP-2 sterol transfer family; Region: SCP2; cl01225 688245002513 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 688245002514 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 688245002515 Sodium:solute symporter family; Region: SSF; cl00456 688245002516 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 688245002517 Protein of unknown function (DUF502); Region: DUF502; cl01107 688245002518 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 688245002519 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 688245002520 dimer interface; other site 688245002521 anticodon binding site; other site 688245002522 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 the...; Region: AspRS_core; cd00777 688245002523 homodimer interface; other site 688245002524 motif 1; other site 688245002525 active site 688245002526 motif 2; other site 688245002527 GAD domain; Region: GAD; pfam02938 688245002528 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 the...; Region: AspRS_core; cd00777 688245002529 motif 3; other site 688245002530 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...; Region: Nudix_Hydrolase; cl00447 688245002531 nudix motif; other site 688245002532 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 688245002533 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 688245002534 active site 688245002535 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 688245002536 EamA-like transporter family; Region: EamA; cl01037 688245002537 LysE type translocator; Region: LysE; cl00565 688245002538 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_6; cd08494 688245002539 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 688245002540 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 688245002541 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245002542 Walker A/P-loop; other site 688245002543 ATP binding site; other site 688245002544 Q-loop/lid; other site 688245002545 ABC transporter signature motif; other site 688245002546 Walker B; other site 688245002547 D-loop; other site 688245002548 H-loop/switch region; other site 688245002549 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 688245002550 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 688245002551 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245002552 Walker A/P-loop; other site 688245002553 ATP binding site; other site 688245002554 Q-loop/lid; other site 688245002555 ABC transporter signature motif; other site 688245002556 Walker B; other site 688245002557 D-loop; other site 688245002558 H-loop/switch region; other site 688245002559 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 688245002560 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...; Region: TM_PBP2; cd06261 688245002561 dimer interface; other site 688245002562 conserved gate region; other site 688245002563 putative PBP binding loops; other site 688245002564 ABC-ATPase subunit interface; other site 688245002565 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...; Region: TM_PBP2; cd06261 688245002566 dimer interface; other site 688245002567 conserved gate region; other site 688245002568 putative PBP binding loops; other site 688245002569 ABC-ATPase subunit interface; other site 688245002570 ferredoxin; Validated; Region: PRK07118 688245002571 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 688245002572 putative active site; other site 688245002573 catalytic residue; other site 688245002574 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 688245002575 5S rRNA interface; other site 688245002576 CTC domain interface; other site 688245002577 L16 interface; other site 688245002578 RatA-like protein; Provisional; Region: PRK15316 688245002579 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 688245002580 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245002581 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 688245002582 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 688245002583 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 688245002584 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 688245002585 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 688245002586 binding surface 688245002587 TPR motif; other site 688245002588 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 688245002589 N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; Region: FpgNei_N; cl03119 688245002590 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 688245002591 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 688245002592 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245002593 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 688245002594 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 688245002595 minor groove reading motif; other site 688245002596 helix-hairpin-helix signature motif; other site 688245002597 substrate binding pocket; other site 688245002598 active site 688245002599 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 688245002600 DNA binding and oxoG recognition site 688245002601 Inner membrane protein CreD; Region: CreD; cl01844 688245002602 sensory histidine kinase CreC; Provisional; Region: PRK11100 688245002603 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245002604 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 trans-...; Region: HisKA; cl00080 688245002605 Domain of unknown function DUF37; Region: DUF37; cl00506 688245002606 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 688245002607 ATP binding site; other site 688245002608 Mg2+ binding site; other site 688245002609 G-X-G motif; other site 688245002610 DNA-binding response regulator CreB; Provisional; Region: PRK11083 688245002611 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 688245002612 active site 688245002613 phosphorylation site 688245002614 intermolecular recognition site; other site 688245002615 dimerization interface; other site 688245002616 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...; Region: trans_reg_C; cd00383 688245002617 DNA binding site 688245002618 P-loop ATPase protein family; Region: ATP_bind_2; cl10035 688245002619 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 688245002620 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 688245002621 Walker A/P-loop; other site 688245002622 ATP binding site; other site 688245002623 Q-loop/lid; other site 688245002624 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 688245002625 ABC transporter signature motif; other site 688245002626 Walker B; other site 688245002627 D-loop; other site 688245002628 H-loop/switch region; other site 688245002629 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 688245002630 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 688245002631 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002632 HrcA protein C terminal domain; Region: HrcA; pfam01628 688245002633 CHASE2 domain; Region: CHASE2; cl01732 688245002634 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 688245002635 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 trans-...; Region: HisKA; cl00080 688245002636 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 688245002637 ATP binding site; other site 688245002638 Mg2+ binding site; other site 688245002639 G-X-G motif; other site 688245002640 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 688245002641 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 688245002642 FecR protein; Region: FecR; pfam04773 688245002643 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 688245002644 active site 688245002645 phosphorylation site 688245002646 intermolecular recognition site; other site 688245002647 dimerization interface; other site 688245002648 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...; Region: trans_reg_C; cd00383 688245002649 DNA binding site 688245002650 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 688245002651 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 688245002652 active site 688245002653 HIGH motif; other site 688245002654 dimer interface; other site 688245002655 KMSKS motif; other site 688245002656 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 688245002657 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 688245002658 active site 688245002659 putative substrate binding region; other site 688245002660 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245002661 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245002662 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245002663 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 688245002664 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 688245002665 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 688245002666 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 688245002667 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245002668 dimerization interface; other site 688245002669 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245002670 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245002671 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 688245002672 DHH family; Region: DHH; pfam01368 688245002673 DHHA1 domain; Region: DHHA1; pfam02272 688245002674 Sulfatase; Region: Sulfatase; cl10460 688245002675 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 688245002676 Sulfatase; Region: Sulfatase; cl10460 688245002677 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 688245002678 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245002679 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002680 LolC/E family; Region: lolCE; TIGR02212 688245002681 Predicted permease; Region: FtsX; cl11418 688245002682 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 688245002683 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 688245002684 Walker A/P-loop; other site 688245002685 ATP binding site; other site 688245002686 Q-loop/lid; other site 688245002687 ABC transporter signature motif; other site 688245002688 Walker B; other site 688245002689 D-loop; other site 688245002690 H-loop/switch region; other site 688245002691 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 688245002692 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 688245002693 putative active site; other site 688245002694 heme pocket; other site 688245002695 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 688245002696 putative active site; other site 688245002697 heme pocket; other site 688245002698 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245002699 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 688245002700 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 688245002701 active site 688245002702 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 688245002703 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; cl12011 688245002704 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 688245002705 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 688245002706 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 688245002707 Walker A motif; other site 688245002708 ATP binding site; other site 688245002709 Walker B motif; other site 688245002710 Tripartite tricarboxylate transporter TctB family; Region: DUF1468; pfam07331 688245002711 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 688245002712 Protein of unknown function (DUF3422); Region: DUF3422; cl02073 688245002713 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245002714 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 688245002715 putative NAD(P) binding site; other site 688245002716 putative active site; other site 688245002717 EamA-like transporter family; Region: EamA; cl01037 688245002718 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245002719 EamA-like transporter family; Region: EamA; cl01037 688245002720 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...; Region: Nudix_Hydrolase; cl00447 688245002721 nudix motif; other site 688245002722 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 688245002723 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 688245002724 PhoU domain; Region: PhoU; pfam01895 688245002725 PhoU domain; Region: PhoU; pfam01895 688245002726 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 688245002727 lipoprotein signal peptidase; Provisional; Region: PRK14787 688245002728 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 688245002729 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245002730 HIGH motif; other site 688245002731 active site 688245002732 nucleotide binding site; other site 688245002733 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 688245002734 active site 688245002735 KMSKS motif; other site 688245002736 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 688245002737 tRNA binding surface; other site 688245002738 anticodon binding site; other site 688245002739 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 688245002740 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 688245002741 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 688245002742 active site 688245002743 Riboflavin kinase; Region: Flavokinase; pfam01687 688245002744 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...; Region: HNHc; cd00085 688245002745 active site 688245002746 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 688245002747 nucleoside/Zn binding site; other site 688245002748 dimer interface; other site 688245002749 catalytic motif; other site 688245002750 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 688245002751 active site 688245002752 homotetramer interface; other site 688245002753 Transthyretin_like. This domain is present in the transthyretin-like protein (TLP) family which includes transthyretin (TTR) and a transthyretin-related protein called 5-hydroxyisourate hydrolase (HIUase). TTR and HIUase are homotetrameric proteins...; Region: Transthyretin_like; cl01000 688245002754 active site 688245002755 homotetramer interface; other site 688245002756 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 688245002757 d-galactonate transporter; Region: 2A0114; TIGR00893 688245002758 putative substrate translocation pore; other site 688245002759 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245002760 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002761 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 688245002762 dimerization interface; other site 688245002763 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 688245002764 Bestrophin; Region: Bestrophin; cl01544 688245002765 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 688245002766 nucleoside/Zn binding site; other site 688245002767 dimer interface; other site 688245002768 catalytic motif; other site 688245002769 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 688245002770 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 688245002771 active site 688245002772 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 688245002773 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245002774 active site 688245002775 hypothetical protein; Provisional; Region: PRK11239 688245002776 Protein of unknown function, DUF480; Region: DUF480; cl01209 688245002777 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 688245002778 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 688245002779 active site 688245002780 substrate binding site; other site 688245002781 cosubstrate binding site; other site 688245002782 catalytic site; other site 688245002783 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 688245002784 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 688245002785 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; cl12011 688245002786 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 688245002787 Di-iron ligands; other site 688245002788 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 688245002789 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245002790 DNA binding site 688245002791 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 688245002792 pyridoxal 5'-phosphate binding site; other site 688245002793 homodimer interface; other site 688245002794 catalytic residue; other site 688245002795 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 688245002796 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 688245002797 thioredoxin reductase; Provisional; Region: PRK10262 688245002798 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245002799 DNA translocase FtsK; Provisional; Region: PRK10263 688245002800 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 688245002801 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245002802 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 688245002803 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 688245002804 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 688245002805 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 688245002806 recombination factor protein RarA; Reviewed; Region: PRK13342 688245002807 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...; Region: AAA; cd00009 688245002808 Walker A motif; other site 688245002809 ATP binding site; other site 688245002810 Walker B motif; other site 688245002811 arginine finger; other site 688245002812 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 688245002813 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 688245002814 TM-ABC transporter signature motif; other site 688245002815 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 688245002816 TM-ABC transporter signature motif; other site 688245002817 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245002818 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245002819 Walker A/P-loop; other site 688245002820 ATP binding site; other site 688245002821 Q-loop/lid; other site 688245002822 ABC transporter signature motif; other site 688245002823 Walker B; other site 688245002824 D-loop; other site 688245002825 H-loop/switch region; other site 688245002826 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245002827 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245002828 Walker A/P-loop; other site 688245002829 ATP binding site; other site 688245002830 Q-loop/lid; other site 688245002831 ABC transporter signature motif; other site 688245002832 Walker B; other site 688245002833 D-loop; other site 688245002834 H-loop/switch region; other site 688245002835 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 688245002836 Phosphate transporter family; Region: PHO4; cl00396 688245002837 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245002838 metal-binding site 688245002839 active site 688245002840 I-site; other site 688245002841 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 688245002842 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 688245002843 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 688245002844 RimM N-terminal domain; Region: RimM; pfam01782 688245002845 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 688245002846 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 688245002847 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 688245002848 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 688245002849 putative active site; other site 688245002850 putative CoA binding site; other site 688245002851 nudix motif; other site 688245002852 metal-binding site 688245002853 CobD/Cbib protein; Region: CobD_Cbib; cl00561 688245002854 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 catalyze...; Region: LT_GEWL; cd00254 688245002855 N-acetyl-D-glucosamine binding site; other site 688245002856 catalytic residue; other site 688245002857 GTPase RsgA; Reviewed; Region: PRK00098 688245002858 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 688245002859 GTPase/OB domain interface; other site 688245002860 GTPase/Zn-binding domain interface; other site 688245002861 GTP/Mg2+ binding site; other site 688245002862 G4 box; other site 688245002863 G5 box; other site 688245002864 G1 box; other site 688245002865 Switch I region; other site 688245002866 G2 box; other site 688245002867 G3 box; other site 688245002868 Switch II region; other site 688245002869 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cd00488 688245002870 aromatic arch; other site 688245002871 DCoH dimer interaction site; other site 688245002872 DCoH /HNF-1 dimer interaction site; other site 688245002873 DCoH tetramer interaction site; other site 688245002874 substrate binding site; other site 688245002875 Peptidase family M48; Region: Peptidase_M48; cl12018 688245002876 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245002877 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 688245002878 ATP binding site; other site 688245002879 Mg++ binding site; other site 688245002880 motif III; other site 688245002881 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 688245002882 nucleotide binding region; other site 688245002883 ATP-binding site; other site 688245002884 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 688245002885 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 688245002886 putative substrate translocation pore; other site 688245002887 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 688245002888 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245002889 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 688245002890 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 the...; Region: IMPDH; cd00381 688245002891 active site 688245002892 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245002893 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245002894 NodT family; Region: outer_NodT; TIGR01845 688245002895 Outer membrane efflux protein; Region: OEP; pfam02321 688245002896 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 688245002897 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...; Region: Biotinyl_lipoyl_domains; cl11404 688245002898 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 688245002899 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 688245002900 putative substrate translocation pore; other site 688245002901 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 688245002902 UvrD/REP helicase; Region: UvrD-helicase; cl14126 688245002903 UvrD/REP helicase; Region: UvrD-helicase; cl14126 688245002904 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 688245002905 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 688245002906 Phosphotransferase enzyme family; Region: APH; pfam01636 688245002907 putative active site; other site 688245002908 putative substrate binding site; other site 688245002909 ATP binding site; other site 688245002910 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 688245002911 DNA polymerase I; Provisional; Region: PRK05755 688245002912 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and...; Region: 53EXOc; cd00008 688245002913 metal binding site I; metal-binding site 688245002914 putative ssDNA interaction site; other site 688245002915 metal binding site II; metal-binding site 688245002916 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of...; Region: 35EXOc; cd00007 688245002917 active site 688245002918 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 688245002919 active site 688245002920 DNA binding site 688245002921 catalytic site; other site 688245002922 AzlC protein; Region: AzlC; cl00570 688245002923 Dienelactone hydrolase family; Region: DLH; pfam01738 688245002924 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 688245002925 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]; Region: COG4753 688245002926 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 688245002927 active site 688245002928 phosphorylation site 688245002929 intermolecular recognition site; other site 688245002930 dimerization interface; other site 688245002931 LytTr DNA-binding domain; Region: LytTR; cl04498 688245002932 Histidine kinase; Region: His_kinase; pfam06580 688245002933 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 688245002934 argininosuccinate lyase; Provisional; Region: PRK00855 688245002935 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 688245002936 active sites 688245002937 tetramer interface; other site 688245002938 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 688245002939 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 688245002940 MG2 domain; Region: A2M_N; pfam01835 688245002941 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 688245002942 Alpha-2-macroglobulin family; Region: A2M; pfam00207 688245002943 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 688245002944 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 688245002945 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245002946 Walker A/P-loop; other site 688245002947 ATP binding site; other site 688245002948 Q-loop/lid; other site 688245002949 ABC transporter signature motif; other site 688245002950 Walker B; other site 688245002951 D-loop; other site 688245002952 H-loop/switch region; other site 688245002953 TOBE domain; Region: TOBE_2; cl01440 688245002954 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 688245002955 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 688245002956 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...; Region: TM_PBP2; cd06261 688245002957 dimer interface; other site 688245002958 conserved gate region; other site 688245002959 putative PBP binding loops; other site 688245002960 ABC-ATPase subunit interface; other site 688245002961 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...; Region: TM_PBP2; cd06261 688245002962 putative PBP binding loops; other site 688245002963 ABC-ATPase subunit interface; other site 688245002964 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 688245002965 Uncharacterized conserved protein [Function unknown]; Region: HdeD; cl01277 688245002966 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 688245002967 Transglycosylase; Region: Transgly; cl07896 688245002968 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245002969 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 688245002970 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245002971 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245002972 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 688245002973 putative effector binding pocket; other site 688245002974 dimerization interface; other site 688245002975 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 688245002976 dimer interface; other site 688245002977 FMN binding site; other site 688245002978 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245002979 EamA-like transporter family; Region: EamA; cl01037 688245002980 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 688245002981 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; cl09108 688245002982 phosphate binding site; other site 688245002983 DNA-binding transcriptional repressor LldR; Provisional; Region: PRK10421 688245002984 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245002985 DNA binding site 688245002986 FCD domain; Region: FCD; cl11656 688245002987 L-lactate permease; Region: Lactate_perm; cl00701 688245002988 L-lactate permease; Region: Lactate_perm; cl00701 688245002989 glycolate transporter; Provisional; Region: PRK09695 688245002990 L-lactate permease; Region: Lactate_perm; cl00701 688245002991 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 688245002992 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; cl09108 688245002993 phosphate binding site; other site 688245002994 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 688245002995 EamA-like transporter family; Region: EamA; cl01037 688245002996 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245002997 Amino acid permease; Region: AA_permease; pfam00324 688245002998 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245002999 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 688245003000 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245003001 Amino acid permease; Region: AA_permease; pfam00324 688245003002 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 688245003003 active site 688245003004 DNA polymerase IV; Validated; Region: PRK02406 688245003005 DNA binding site 688245003006 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 688245003007 PAS fold; Region: PAS_3; pfam08447 688245003008 putative active site; other site 688245003009 heme pocket; other site 688245003010 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245003011 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245003012 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 688245003013 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 688245003014 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 688245003015 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245003016 Protein of unknown function (DUF328); Region: DUF328; cl01143 688245003017 ribonuclease E; Reviewed; Region: rne; PRK10811 688245003018 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 688245003019 homodimer interface; other site 688245003020 oligonucleotide binding site; other site 688245003021 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 688245003022 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; cl09940 688245003023 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 688245003024 active site 688245003025 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 688245003026 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 688245003027 motif II; other site 688245003028 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)...; Region: Rieske; cd03467 688245003029 iron-sulfur cluster; other site 688245003030 [2Fe-2S] cluster binding site; other site 688245003031 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 688245003032 tandem repeat interface; other site 688245003033 oligomer interface; other site 688245003034 active site residues 688245003035 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245003036 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 688245003037 active site 688245003038 dimer interface; other site 688245003039 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 688245003040 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 688245003041 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 688245003042 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 688245003043 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 688245003044 dimer interface; other site 688245003045 active site 688245003046 CoA binding pocket; other site 688245003047 Acyl transferase domain; Region: Acyl_transf_1; cl08282 688245003048 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 688245003049 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003050 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 688245003051 Phosphopantetheine attachment site; Region: PP-binding; cl09936 688245003052 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 688245003053 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 688245003054 dimer interface; other site 688245003055 active site 688245003056 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 688245003057 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245003058 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...; Region: Sigma70_r4; cd06171 688245003059 DNA binding residues 688245003060 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 688245003061 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 688245003062 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 688245003063 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 C-...; Region: PDZ_serine_protease; cd00987 688245003064 protein binding site; other site 688245003065 GTP-binding protein LepA; Provisional; Region: PRK05433 688245003066 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 688245003067 G1 box; other site 688245003068 putative GEF interaction site; other site 688245003069 GTP/Mg2+ binding site; other site 688245003070 Switch I region; other site 688245003071 G2 box; other site 688245003072 G3 box; other site 688245003073 Switch II region; other site 688245003074 G4 box; other site 688245003075 G5 box; other site 688245003076 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-...; Region: lepA_II; cd03699 688245003077 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 688245003078 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 688245003079 signal peptidase I; Provisional; Region: PRK10861 688245003080 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 688245003081 Catalytic site; other site 688245003082 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 688245003083 ribonuclease III; Reviewed; Region: rnc; PRK00102 688245003084 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 post-...; Region: RIBOc; cd00593 688245003085 dimerization interface; other site 688245003086 active site 688245003087 metal-binding site 688245003088 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...; Region: DSRM; cd00048 688245003089 dsRNA binding site; other site 688245003090 GTPase Era; Reviewed; Region: era; PRK00089 688245003091 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 688245003092 G1 box; other site 688245003093 GTP/Mg2+ binding site; other site 688245003094 Switch I region; other site 688245003095 G2 box; other site 688245003096 Switch II region; other site 688245003097 G3 box; other site 688245003098 G4 box; other site 688245003099 G5 box; other site 688245003100 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 688245003101 Recombination protein O N terminal; Region: RecO_N; pfam11967 688245003102 Recombination protein O C terminal; Region: RecO_C; pfam02565 688245003103 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 688245003104 active site 688245003105 hydrophilic channel; other site 688245003106 dimerization interface; other site 688245003107 catalytic residues; other site 688245003108 active site lid 688245003109 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 688245003110 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 688245003111 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 688245003112 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245003113 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 688245003114 6-phosphofructokinase; Provisional; Region: PRK03202 688245003115 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases...; Region: PFK; cl00204 688245003116 active site 688245003117 ADP/pyrophosphate binding site; other site 688245003118 dimerization interface; other site 688245003119 allosteric effector site; other site 688245003120 fructose-1,6-bisphosphate binding site; other site 688245003121 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 688245003122 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 688245003123 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245003124 Mechanosensitive ion channel; Region: MS_channel; pfam00924 688245003125 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 688245003126 active site 688245003127 phosphorylation site 688245003128 intermolecular recognition site; other site 688245003129 dimerization interface; other site 688245003130 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245003131 metal-binding site 688245003132 active site 688245003133 I-site; other site 688245003134 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 688245003135 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-...; Region: LysRS_N; cd04322 688245003136 dimer interface; other site 688245003137 putative anticodon binding site; other site 688245003138 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 688245003139 motif 1; other site 688245003140 active site 688245003141 motif 2; other site 688245003142 motif 3; other site 688245003143 Found in ATP-dependent protease La (LON); Region: LON; cl01056 688245003144 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 688245003145 YGGT family; Region: YGGT; cl00508 688245003146 YGGT family; Region: YGGT; cl00508 688245003147 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 688245003148 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245003149 tryptophan synthase; Region: PLN02591 688245003150 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...; Region: Tryptophan_synthase_alpha; cd04724 688245003151 substrate binding site; other site 688245003152 active site 688245003153 catalytic residues; other site 688245003154 heterodimer interface; other site 688245003155 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 688245003156 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 688245003157 pyridoxal 5'-phosphate binding site; other site 688245003158 catalytic residue; other site 688245003159 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 monomeric...; Region: PRAI; cd00405 688245003160 active site 688245003161 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 688245003162 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 688245003163 dimerization interface 3.5A; other site 688245003164 active site 688245003165 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 688245003166 FimV N-terminal domain; Region: FimV_core; TIGR03505 688245003167 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 688245003168 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 688245003169 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 688245003170 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003171 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 688245003172 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 688245003173 isocitrate dehydrogenase; Validated; Region: PRK06451 688245003174 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 3-...; Region: IPMI_Swivel; cd01577 688245003175 substrate binding site; other site 688245003176 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 688245003177 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 688245003178 substrate binding site; other site 688245003179 ligand binding site; other site 688245003180 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245003181 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003182 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 688245003183 putative dimerization interface; other site 688245003184 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245003185 Sel1 repeat; Region: Sel1; cl02723 688245003186 Sel1 repeat; Region: Sel1; cl02723 688245003187 Sel1 repeat; Region: Sel1; cl02723 688245003188 Sel1 repeat; Region: Sel1; cl02723 688245003189 Sel1 repeat; Region: Sel1; cl02723 688245003190 chaperone protein DnaJ; Provisional; Region: PRK10767 688245003191 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...; Region: DnaJ; cd06257 688245003192 DnaJ C terminal region; Region: DnaJ_C; pfam01556 688245003193 DnaJ C terminal region; Region: DnaJ_C; pfam01556 688245003194 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 688245003195 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 688245003196 dimer interface; other site 688245003197 hsp70 (ATPase domain) interactions; other site 688245003198 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 688245003199 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 688245003200 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 688245003201 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 688245003202 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 688245003203 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 688245003204 replicative DNA helicase; Region: DnaB; TIGR00665 688245003205 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 688245003206 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 688245003207 Walker A motif; other site 688245003208 ATP binding site; other site 688245003209 Walker B motif; other site 688245003210 DNA binding loops 688245003211 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 688245003212 PIN domain; Region: PIN; cl09128 688245003213 PhoH-like protein; Region: PhoH; cl12134 688245003214 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...; Region: PRX_BCP; cd03017 688245003215 catalytic triad; other site 688245003216 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 688245003217 alanine aminotransferase; Provisional; Region: PTZ00377 688245003218 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 688245003219 pyridoxal 5'-phosphate binding site; other site 688245003220 homodimer interface; other site 688245003221 catalytic residue; other site 688245003222 homoserine dehydrogenase; Provisional; Region: PRK06349 688245003223 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003224 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 688245003225 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 688245003226 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 688245003227 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 688245003228 pyridoxal 5'-phosphate binding site; other site 688245003229 catalytic residue; other site 688245003230 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 688245003231 Walker A motif; other site 688245003232 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 688245003233 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 688245003234 dimer interface; other site 688245003235 putative functional site; other site 688245003236 putative MPT binding site; other site 688245003237 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 688245003238 MoaE interaction surface; other site 688245003239 MoeB interaction surface; other site 688245003240 thiocarboxylated glycine; other site 688245003241 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; cl09110 688245003242 Recombinase; Region: Recombinase; pfam07508 688245003243 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 688245003244 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245003245 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 688245003246 MoaE homodimer interface; other site 688245003247 MoaD interaction; other site 688245003248 active site residues 688245003249 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245003250 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 688245003251 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 688245003252 Clp amino terminal domain; Region: Clp_N; pfam02861 688245003253 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...; Region: AAA; cd00009 688245003254 Walker A motif; other site 688245003255 ATP binding site; other site 688245003256 Walker B motif; other site 688245003257 arginine finger; other site 688245003258 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...; Region: AAA; cd00009 688245003259 Walker A motif; other site 688245003260 ATP binding site; other site 688245003261 Walker B motif; other site 688245003262 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 688245003263 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 688245003264 NAD(P) binding site; other site 688245003265 catalytic residues; other site 688245003266 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245003267 Coenzyme A binding pocket; other site 688245003268 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 688245003269 S-adenosylmethionine binding site; other site 688245003270 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 688245003271 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...; Region: DUS_like_FMN; cd02801 688245003272 FMN binding site; other site 688245003273 active site 688245003274 catalytic residues; other site 688245003275 substrate binding site; other site 688245003276 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245003277 active site 688245003278 signature motif; other site 688245003279 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245003280 active site 688245003281 signature motif; other site 688245003282 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 688245003283 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 688245003284 catalytic motif; other site 688245003285 Zn binding site; other site 688245003286 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 5,10-...; Region: DHFR; cl00161 688245003287 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 688245003288 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 688245003289 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 688245003290 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 688245003291 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 688245003292 Type II transport protein GspH; Region: GspH; pfam12019 688245003293 Type II transport protein GspH; Region: GspH; pfam12019 688245003294 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...; Region: Ribosomal_S15p_S13e; cd00353 688245003295 16S/18S rRNA binding site; other site 688245003296 S13e-L30e interaction site; other site 688245003297 25S rRNA binding site; other site 688245003298 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 688245003299 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 688245003300 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 688245003301 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 688245003302 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 688245003303 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 688245003304 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 688245003305 putative nucleic acid binding region; other site 688245003306 G-X-X-G motif; other site 688245003307 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 688245003308 RNA binding site; other site 688245003309 domain interface; other site 688245003310 potential frameshift: common BLAST hit: gi|160900615|ref|YP_001566197.1| PIG3 family NAD(P)H quinone oxidoreductase 688245003311 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 688245003312 NAD(P) binding site; other site 688245003313 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 688245003314 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 688245003315 substrate binding site; other site 688245003316 dimer interface; other site 688245003317 catalytic triad; other site 688245003318 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 688245003319 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 688245003320 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 688245003321 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 688245003322 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 688245003323 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...; Region: TRX_Fd_NuoE; cd03064 688245003324 putative dimer interface; other site 688245003325 [2Fe-2S] cluster binding site; other site 688245003326 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 688245003327 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 688245003328 SLBB domain; Region: SLBB; pfam10531 688245003329 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 688245003330 NADH dehydrogenase subunit G; Validated; Region: PRK09129 688245003331 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 688245003332 catalytic loop; other site 688245003333 iron binding site; other site 688245003334 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 688245003335 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...; Region: MopB_NDH-1_NuoG2; cd02772 688245003336 NADH dehydrogenase; Region: NADHdh; cl00469 688245003337 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 688245003338 4Fe-4S binding domain; Region: Fer4; pfam00037 688245003339 4Fe-4S binding domain; Region: Fer4; pfam00037 688245003340 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 688245003341 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 688245003342 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 688245003343 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 688245003344 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 688245003345 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 688245003346 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 688245003347 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 688245003348 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 688245003349 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 688245003350 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 688245003351 Protein of unknown function (DUF1178); Region: DUF1178; cl02196 688245003352 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 688245003353 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 688245003354 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...; Region: Sigma70_r4; cd06171 688245003355 DNA binding residues 688245003356 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 688245003357 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 688245003358 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245003359 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245003360 Walker A/P-loop; other site 688245003361 ATP binding site; other site 688245003362 Q-loop/lid; other site 688245003363 ABC transporter signature motif; other site 688245003364 Walker B; other site 688245003365 D-loop; other site 688245003366 H-loop/switch region; other site 688245003367 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245003368 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245003369 Walker A/P-loop; other site 688245003370 ATP binding site; other site 688245003371 Q-loop/lid; other site 688245003372 ABC transporter signature motif; other site 688245003373 Walker B; other site 688245003374 D-loop; other site 688245003375 H-loop/switch region; other site 688245003376 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245003377 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 688245003378 putative ligand binding site; other site 688245003379 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 688245003380 TM-ABC transporter signature motif; other site 688245003381 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 688245003382 TM-ABC transporter signature motif; other site 688245003383 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 688245003384 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 688245003385 Trp docking motif; other site 688245003386 active site 688245003387 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 688245003388 Trp docking motif; other site 688245003389 active site 688245003390 'Velcro' closure; other site 688245003391 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 688245003392 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245003393 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 688245003394 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 688245003395 Predicted permease; Region: FtsX; cl11418 688245003396 Predicted permease; Region: FtsX; cl11418 688245003397 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 688245003398 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 688245003399 Walker A/P-loop; other site 688245003400 ATP binding site; other site 688245003401 Q-loop/lid; other site 688245003402 ABC transporter signature motif; other site 688245003403 Walker B; other site 688245003404 D-loop; other site 688245003405 H-loop/switch region; other site 688245003406 IPP transferase; Region: IPPT; cl00403 688245003407 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 688245003408 Sulfatase; Region: Sulfatase; cl10460 688245003409 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 688245003410 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 688245003411 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 688245003412 putative substrate translocation pore; other site 688245003413 Esterase/lipase [General function prediction only]; Region: COG1647 688245003414 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; cl12031 688245003415 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 688245003416 substrate binding site; other site 688245003417 hypothetical protein; Provisional; Region: PRK10318 688245003418 Cupin domain; Region: Cupin_2; cl09118 688245003419 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 688245003420 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 688245003421 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 688245003422 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245003423 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; cl11391 688245003424 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 688245003425 glutamate dehydrogenase; Provisional; Region: PRK09414 688245003426 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 688245003427 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 688245003428 NAD(P) binding site; other site 688245003429 benzoate transport; Region: 2A0115; TIGR00895 688245003430 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 688245003431 putative substrate translocation pore; other site 688245003432 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 688245003433 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245003434 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 688245003435 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 688245003436 putative active site; other site 688245003437 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 688245003438 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 688245003439 ATP binding site; other site 688245003440 Mg2+ binding site; other site 688245003441 G-X-G motif; other site 688245003442 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 688245003443 ATP binding site; other site 688245003444 MutL C terminal dimerization domain; Region: MutL_C; cl07336 688245003445 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 688245003446 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 688245003447 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 688245003448 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 688245003449 active site 688245003450 metal-binding site 688245003451 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 688245003452 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 688245003453 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 688245003454 Membrane transport protein; Region: Mem_trans; cl09117 688245003455 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 688245003456 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 688245003457 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 of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 688245003458 Int/Topo IB signature motif; other site 688245003459 active site 688245003460 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 688245003461 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 688245003462 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 688245003463 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 688245003464 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245003465 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 688245003466 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 688245003467 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245003468 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 688245003469 dinuclear metal binding motif; other site 688245003470 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 688245003471 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 688245003472 trimer interface; other site 688245003473 putative metal binding site; other site 688245003474 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 688245003475 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 688245003476 dimerization interface; other site 688245003477 domain crossover interface; other site 688245003478 redox-dependent activation switch; other site 688245003479 Septum formation initiator; Region: DivIC; cl11433 688245003480 enolase; Provisional; Region: eno; PRK00077 688245003481 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 688245003482 dimer interface; other site 688245003483 metal-binding site 688245003484 substrate binding pocket; other site 688245003485 NeuB family; Region: NeuB; cl00496 688245003486 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 688245003487 CTP synthetase; Validated; Region: pyrG; PRK05380 688245003488 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...; Region: CTGs; cd03113 688245003489 UTP binding site; other site 688245003490 active site 688245003491 Catalytic site; other site 688245003492 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 688245003493 active site 688245003494 putative oxyanion hole; other site 688245003495 catalytic triad; other site 688245003496 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 688245003497 Flavoprotein; Region: Flavoprotein; cl08021 688245003498 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 688245003499 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 688245003500 trimer interface; other site 688245003501 active site 688245003502 sensor protein PhoQ; Provisional; Region: PRK10815 688245003503 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 688245003504 ATP binding site; other site 688245003505 Mg2+ binding site; other site 688245003506 G-X-G motif; other site 688245003507 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245003508 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 688245003509 active site 688245003510 phosphorylation site 688245003511 intermolecular recognition site; other site 688245003512 dimerization interface; other site 688245003513 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...; Region: trans_reg_C; cd00383 688245003514 DNA binding site 688245003515 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 688245003516 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245003517 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 688245003518 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 688245003519 NAD(P) binding site; other site 688245003520 catalytic residues; other site 688245003521 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245003522 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245003523 Walker A/P-loop; other site 688245003524 ATP binding site; other site 688245003525 Q-loop/lid; other site 688245003526 ABC transporter signature motif; other site 688245003527 Walker B; other site 688245003528 D-loop; other site 688245003529 H-loop/switch region; other site 688245003530 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245003531 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245003532 Walker A/P-loop; other site 688245003533 ATP binding site; other site 688245003534 Q-loop/lid; other site 688245003535 ABC transporter signature motif; other site 688245003536 Walker B; other site 688245003537 D-loop; other site 688245003538 H-loop/switch region; other site 688245003539 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 688245003540 TM-ABC transporter signature motif; other site 688245003541 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 688245003542 TM-ABC transporter signature motif; other site 688245003543 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245003544 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_5; cd06338 688245003545 putative ligand binding site; other site 688245003546 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 688245003547 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245003548 FAD binding domain; Region: FAD_binding_4; pfam01565 688245003549 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 688245003550 Cytochrome c; Region: Cytochrom_C; cl11414 688245003551 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 688245003552 NAD(P) binding site; other site 688245003553 catalytic residues; other site 688245003554 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 688245003555 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245003556 Cupin superfamily protein; Region: Cupin_4; pfam08007 688245003557 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 688245003558 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 688245003559 Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue...; Region: DHDPS; cd00950 688245003560 dihydrodipicolinate synthase; Region: dapA; TIGR00674 688245003561 dimer interface; other site 688245003562 active site 688245003563 catalytic residue; other site 688245003564 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; cl12011 688245003565 short chain dehydrogenase; Provisional; Region: PRK06181 688245003566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003567 NAD(P) binding site; other site 688245003568 active site 688245003569 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245003570 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 688245003571 putative substrate translocation pore; other site 688245003572 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 688245003573 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 688245003574 ATP binding site; other site 688245003575 Mg2+ binding site; other site 688245003576 G-X-G motif; other site 688245003577 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 688245003578 anchoring element; other site 688245003579 dimer interface; other site 688245003580 ATP binding site; other site 688245003581 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 688245003582 active site 688245003583 metal-binding site 688245003584 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 688245003585 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 catalyze...; Region: LT_GEWL; cd00254 688245003586 N-acetyl-D-glucosamine binding site; other site 688245003587 catalytic residue; other site 688245003588 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 688245003589 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 in...; Region: TOP4c; cd00187 688245003590 CAP-like domain; other site 688245003591 active site 688245003592 primary dimer interface; other site 688245003593 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245003594 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245003595 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003596 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 688245003597 dimerization interface; other site 688245003598 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 688245003599 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 688245003600 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 688245003601 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 688245003602 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 688245003603 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 688245003604 pyridoxal binding site; other site 688245003605 dimer interface; other site 688245003606 ATP binding site; other site 688245003607 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 688245003608 homotrimer interaction site; other site 688245003609 putative active site; other site 688245003610 Competence protein; Region: Competence; cl00471 688245003611 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245003612 Uncharacterized conserved protein [Function unknown]; Region: COG2308 688245003613 Domain of unknown function (DUF404); Region: DUF404; pfam04169 688245003614 Domain of unknown function (DUF407); Region: DUF407; pfam04174 688245003615 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 688245003616 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 688245003617 Ferritin-like domain; Region: Ferritin; pfam00210 688245003618 heme binding site; other site 688245003619 ferroxidase pore; other site 688245003620 ferroxidase diiron center; other site 688245003621 peroxiredoxin; Region: AhpC; TIGR03137 688245003622 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...; Region: PRX_Typ2cys; cd03015 688245003623 dimer interface; other site 688245003624 decamer (pentamer of dimers) interface; other site 688245003625 catalytic triad; other site 688245003626 peroxidatic and resolving cysteines; other site 688245003627 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 688245003628 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...; Region: AhpF_NTD_N; cd02974 688245003629 catalytic residue; other site 688245003630 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 688245003631 catalytic residues; other site 688245003632 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245003633 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 688245003634 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 688245003635 N-terminal plug; other site 688245003636 ligand-binding site; other site 688245003637 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 688245003638 ChuX-like family; Region: DUF1008; cl01509 688245003639 ChuX-like family; Region: DUF1008; cl01509 688245003640 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...; Region: TroA-like; cl00262 688245003641 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 688245003642 intersubunit interface; other site 688245003643 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...; Region: TM_ABC_iron-siderophores_like; cl00462 688245003644 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...; Region: TM_ABC_iron-siderophores_like; cd06550 688245003645 ABC-ATPase subunit interface; other site 688245003646 dimer interface; other site 688245003647 putative PBP binding regions; other site 688245003648 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 688245003649 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245003650 Walker A/P-loop; other site 688245003651 ATP binding site; other site 688245003652 Q-loop/lid; other site 688245003653 ABC transporter signature motif; other site 688245003654 Walker B; other site 688245003655 D-loop; other site 688245003656 H-loop/switch region; other site 688245003657 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 688245003658 transcriptional regulator; Provisional; Region: PRK10632 688245003659 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003660 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 688245003661 putative effector binding pocket; other site 688245003662 dimerization interface; other site 688245003663 Domain of unknown function (DUF299); Region: DUF299; cl00780 688245003664 phosphoenolpyruvate synthase; Validated; Region: PRK06464 688245003665 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 688245003666 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 688245003667 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245003668 Predicted membrane protein [Function unknown]; Region: COG4327; cl01781 688245003669 Sodium:solute symporter family; Region: SSF; cl00456 688245003670 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 688245003671 Sodium:solute symporter family; Region: SSF; cl00456 688245003672 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245003673 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003674 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 688245003675 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003676 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 688245003677 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 688245003678 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 688245003679 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 688245003680 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 688245003681 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 688245003682 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245003683 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 688245003684 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...; Region: Sigma70_r4; cd06171 688245003685 DNA binding residues 688245003686 DNA primase, catalytic core; Region: dnaG; TIGR01391 688245003687 CHC2 zinc finger; Region: zf-CHC2; cl02597 688245003688 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 688245003689 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 688245003690 active site 688245003691 metal-binding site 688245003692 interdomain interaction site; other site 688245003693 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 688245003694 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 688245003695 acyl-CoA synthetase; Validated; Region: PRK08162 688245003696 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245003697 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2908 688245003698 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 688245003699 putative active site; other site 688245003700 putative metal binding site; other site 688245003701 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 688245003702 active site 688245003703 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 688245003704 active site 688245003705 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 688245003706 TPR motif; other site 688245003707 binding surface 688245003708 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 688245003709 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 688245003710 active site 688245003711 HIGH motif; other site 688245003712 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 688245003713 KMSKS motif; other site 688245003714 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 688245003715 tRNA binding surface; other site 688245003716 anticodon binding site; other site 688245003717 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 688245003718 endonuclease III; Region: ENDO3c; smart00478 688245003719 minor groove reading motif; other site 688245003720 helix-hairpin-helix signature motif; other site 688245003721 substrate binding pocket; other site 688245003722 active site 688245003723 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245003724 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 688245003725 Ligand Binding Site; other site 688245003726 aspartate kinase; Reviewed; Region: PRK06635 688245003727 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 688245003728 putative nucleotide binding site; other site 688245003729 putative catalytic residues; other site 688245003730 putative Mg ion binding site; other site 688245003731 putative aspartate binding site; other site 688245003732 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 688245003733 putative allosteric regulatory site; other site 688245003734 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 688245003735 putative allosteric regulatory residue; other site 688245003736 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 688245003737 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 688245003738 active site 688245003739 uracil binding; other site 688245003740 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 688245003741 active site 688245003742 substrate binding site; other site 688245003743 Mg2+ binding site; other site 688245003744 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 688245003745 RNA binding surface; other site 688245003746 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 688245003747 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 trans-...; Region: HisKA; cd00082 688245003748 dimer interface; other site 688245003749 phosphorylation site 688245003750 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 688245003751 ATP binding site; other site 688245003752 Mg2+ binding site; other site 688245003753 G-X-G motif; other site 688245003754 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 688245003755 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 688245003756 active site 688245003757 phosphorylation site 688245003758 intermolecular recognition site; other site 688245003759 dimerization interface; other site 688245003760 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...; Region: trans_reg_C; cd00383 688245003761 DNA binding site 688245003762 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 688245003763 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 688245003764 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 688245003765 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...; Region: AAA; cd00009 688245003766 Walker A motif; other site 688245003767 ATP binding site; other site 688245003768 Walker B motif; other site 688245003769 arginine finger; other site 688245003770 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245003771 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 688245003772 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 688245003773 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245003774 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...; Region: metallo-dependent_hydrolases; cl00281 688245003775 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245003776 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria; Region: PBP1_SBP_like_2; cd06328 688245003777 putative ligand binding site; other site 688245003778 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245003779 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245003780 Walker A/P-loop; other site 688245003781 ATP binding site; other site 688245003782 Q-loop/lid; other site 688245003783 ABC transporter signature motif; other site 688245003784 Walker B; other site 688245003785 D-loop; other site 688245003786 H-loop/switch region; other site 688245003787 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245003788 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245003789 Walker A/P-loop; other site 688245003790 ATP binding site; other site 688245003791 Q-loop/lid; other site 688245003792 ABC transporter signature motif; other site 688245003793 Walker B; other site 688245003794 D-loop; other site 688245003795 H-loop/switch region; other site 688245003796 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 688245003797 TM-ABC transporter signature motif; other site 688245003798 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 688245003799 TM-ABC transporter signature motif; other site 688245003800 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 688245003801 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245003802 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; cl12031 688245003803 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; cl12031 688245003804 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 688245003805 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 688245003806 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 688245003807 active site residue 688245003808 putative inner membrane protein; Provisional; Region: PRK11099 688245003809 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 688245003810 active site residue 688245003811 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 688245003812 active site residue 688245003813 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245003814 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245003815 xanthine dehydrogenase D subunit; Region: pucD; TIGR03196 688245003816 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 688245003817 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245003818 xanthine dehydrogenase C subunit; Region: pucC; TIGR03199 688245003819 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 688245003820 nucleoside/Zn binding site; other site 688245003821 dimer interface; other site 688245003822 catalytic motif; other site 688245003823 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...; Region: TM_PBP2; cl00427 688245003824 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245003825 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245003826 Walker A/P-loop; other site 688245003827 ATP binding site; other site 688245003828 Q-loop/lid; other site 688245003829 ABC transporter signature motif; other site 688245003830 Walker B; other site 688245003831 D-loop; other site 688245003832 H-loop/switch region; other site 688245003833 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...; Region: PBPb; cd00134 688245003834 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 688245003835 substrate binding pocket; other site 688245003836 membrane-bound complex binding site; other site 688245003837 hinge residues; other site 688245003838 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; cl12031 688245003839 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245003840 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 688245003841 flavanone-3-hydroxylase; Provisional; Region: PLN03176 688245003842 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245003843 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245003844 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003845 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 688245003846 dimerization interface; other site 688245003847 ferrochelatase; Reviewed; Region: hemH; PRK00035 688245003848 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 688245003849 C-terminal domain interface; other site 688245003850 active site 688245003851 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 688245003852 active site 688245003853 N-terminal domain interface; other site 688245003854 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; cl11391 688245003855 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 688245003856 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 688245003857 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 688245003858 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245003859 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 688245003860 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 688245003861 catalytic residues; other site 688245003862 substrate binding pocket; other site 688245003863 substrate-Mg2+ binding site; other site 688245003864 aspartate-rich region 1; other site 688245003865 aspartate-rich region 2; other site 688245003866 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 688245003867 active site lid residues 688245003868 substrate binding pocket; other site 688245003869 catalytic residues; other site 688245003870 substrate-Mg2+ binding site; other site 688245003871 aspartate-rich region 1; other site 688245003872 aspartate-rich region 2; other site 688245003873 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245003874 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 688245003875 trigger factor; Provisional; Region: tig; PRK01490 688245003876 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245003877 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 688245003878 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 688245003879 oligomer interface; other site 688245003880 active site residues 688245003881 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 688245003882 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 688245003883 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...; Region: AAA; cd00009 688245003884 Walker A motif; other site 688245003885 ATP binding site; other site 688245003886 Walker B motif; other site 688245003887 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 688245003888 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 688245003889 Found in ATP-dependent protease La (LON); Region: LON; cl01056 688245003890 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...; Region: AAA; cd00009 688245003891 Walker A motif; other site 688245003892 ATP binding site; other site 688245003893 Walker B motif; other site 688245003894 arginine finger; other site 688245003895 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 688245003896 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 688245003897 N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 688245003898 THF binding site; other site 688245003899 C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 688245003900 substrate binding site; other site 688245003901 THF binding site; other site 688245003902 zinc-binding site; other site 688245003903 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245003904 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245003905 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 688245003906 putative dimerization interface; other site 688245003907 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245003908 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245003909 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245003910 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 688245003911 conserved cys residue; other site 688245003912 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 688245003913 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245003914 DNA binding site 688245003915 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 688245003916 pyridoxal 5'-phosphate binding site; other site 688245003917 homodimer interface; other site 688245003918 catalytic residue; other site 688245003919 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 688245003920 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 688245003921 tetramer interface; other site 688245003922 active site 688245003923 Mg2+/Mn2+ binding site; other site 688245003924 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 688245003925 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 688245003926 Propionate catabolism activator; Region: PrpR_N; pfam06506 688245003927 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 688245003928 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 688245003929 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...; Region: AAA; cd00009 688245003930 Walker A motif; other site 688245003931 ATP binding site; other site 688245003932 Walker B motif; other site 688245003933 arginine finger; other site 688245003934 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245003935 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 688245003936 PAS fold; Region: PAS_3; pfam08447 688245003937 putative active site; other site 688245003938 heme pocket; other site 688245003939 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245003940 metal-binding site 688245003941 active site 688245003942 I-site; other site 688245003943 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 688245003944 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 688245003945 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 688245003946 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 688245003947 substrate binding site; other site 688245003948 ligand binding site; other site 688245003949 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 688245003950 substrate binding site; other site 688245003951 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245003952 DNA binding site 688245003953 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (...; Region: Ec2MCS_like_1; cd06117 688245003954 dimer interface; other site 688245003955 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 688245003956 active site 688245003957 oxalacetate/citrate binding site; other site 688245003958 citrylCoA binding site; other site 688245003959 coenzyme A binding site; other site 688245003960 catalytic triad; other site 688245003961 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245003962 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 688245003963 Domain of unknown function (DUF955); Region: DUF955; cl01076 688245003964 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 688245003965 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245003966 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245003967 NAD(P) binding site; other site 688245003968 active site 688245003969 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245003970 classical (c) SDRs; Region: SDR_c; cd05233 688245003971 NAD(P) binding site; other site 688245003972 active site 688245003973 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245003974 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 688245003975 FMN binding site; other site 688245003976 active site 688245003977 substrate binding site; other site 688245003978 catalytic residue; other site 688245003979 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 688245003980 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 688245003981 Coenzyme A transferase; Region: CoA_trans; cl00773 688245003982 Coenzyme A transferase; Region: CoA_trans; cl00773 688245003983 enoyl-CoA hydratase; Provisional; Region: PRK08290 688245003984 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 688245003985 substrate binding site; other site 688245003986 oxyanion hole (OAH) forming residues; other site 688245003987 trimer interface; other site 688245003988 2-nitropropane dioxygenase; Region: NPD; pfam03060 688245003989 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...; Region: NPD_like; cd04730 688245003990 FMN binding site; other site 688245003991 substrate binding site; other site 688245003992 putative catalytic residue; other site 688245003993 enoyl-CoA hydratase; Provisional; Region: PRK07938 688245003994 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 688245003995 substrate binding site; other site 688245003996 oxyanion hole (OAH) forming residues; other site 688245003997 trimer interface; other site 688245003998 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 688245003999 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 688245004000 FAD binding site; other site 688245004001 substrate binding site; other site 688245004002 catalytic base; other site 688245004003 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004004 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004005 active site 688245004006 acetyl-CoA acetyltransferase; Provisional; Region: PRK07801 688245004007 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 688245004008 dimer interface; other site 688245004009 active site 688245004010 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; cl11426 688245004011 Amidase; Region: Amidase; pfam01425 688245004012 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 688245004013 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; cl11426 688245004014 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 688245004015 homodimer interface; other site 688245004016 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245004017 NAD binding site; other site 688245004018 active site 688245004019 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245004020 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 688245004021 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 688245004022 active site 688245004023 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245004024 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004025 active site 688245004026 short chain dehydrogenase; Provisional; Region: PRK07831 688245004027 classical (c) SDRs; Region: SDR_c; cd05233 688245004028 NAD(P) binding site; other site 688245004029 active site 688245004030 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 688245004031 putative active site; other site 688245004032 putative catalytic site; other site 688245004033 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 688245004034 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 688245004035 dimer interface; other site 688245004036 active site 688245004037 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...; Region: LuxR_C_like; cd06170 688245004038 DNA binding residues 688245004039 dimerization interface; other site 688245004040 Cache domain; Region: Cache_1; pfam02743 688245004041 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004042 metal-binding site 688245004043 active site 688245004044 I-site; other site 688245004045 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245004046 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245004047 classical (c) SDRs; Region: SDR_c; cd05233 688245004048 NAD(P) binding site; other site 688245004049 active site 688245004050 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 688245004051 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 688245004052 dimer interface; other site 688245004053 active site 688245004054 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 688245004055 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 688245004056 substrate binding site; other site 688245004057 oxyanion hole (OAH) forming residues; other site 688245004058 trimer interface; other site 688245004059 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004060 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245004061 choline dehydrogenase; Validated; Region: PRK02106 688245004062 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 688245004063 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 688245004064 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245004065 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004066 active site 688245004067 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 688245004068 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004069 active site 688245004070 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 688245004071 putative substrate translocation pore; other site 688245004072 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245004073 acyl-CoA synthetase; Validated; Region: PRK07798 688245004074 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004075 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004076 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 688245004077 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 688245004078 active site 688245004079 putative substrate binding pocket; other site 688245004080 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...; Region: metallo-dependent_hydrolases; cl00281 688245004081 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 688245004082 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245004083 putative substrate translocation pore; other site 688245004084 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 688245004085 [2Fe-2S] cluster binding site; other site 688245004086 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245004087 classical (c) SDRs; Region: SDR_c; cd05233 688245004088 NAD(P) binding site; other site 688245004089 active site 688245004090 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 688245004091 putative substrate translocation pore; other site 688245004092 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 688245004093 NAD(P) binding site; other site 688245004094 catalytic residues; other site 688245004095 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245004096 classical (c) SDRs; Region: SDR_c; cd05233 688245004097 NAD(P) binding site; other site 688245004098 active site 688245004099 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245004100 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004101 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 688245004102 putative effector binding pocket; other site 688245004103 dimerization interface; other site 688245004104 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 688245004105 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 688245004106 catalytic residues; other site 688245004107 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245004108 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 688245004109 Aminoglycoside/hydroxyurea antibiotic resistance kinase; Region: APH_6_hur; cl10490 688245004110 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 688245004111 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245004112 Coenzyme A binding pocket; other site 688245004113 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 688245004114 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245004115 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...; Region: OYE_like_FMN_family; cd02803 688245004116 active site 688245004117 FMN binding site; other site 688245004118 substrate binding site; other site 688245004119 putative catalytic residue; other site 688245004120 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 688245004121 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004122 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004123 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245004124 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 688245004125 active site 688245004126 FMN binding site; other site 688245004127 2,4-decadienoyl-CoA binding site; other site 688245004128 catalytic residue; other site 688245004129 4Fe-4S cluster binding site; other site 688245004130 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 688245004131 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004132 alpha hydroxysteroid dehydrogenase (3alpha_HSD), classical (c) SDRs; Region: 3alpha_HSD_SDR_c; cd05328 688245004133 tropinone reductase; Provisional; Region: PRK09242 688245004134 NAD binding site; other site 688245004135 active site 688245004136 homodimer interface; other site 688245004137 ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon...; Region: ketosteroid_isomerase; cd00781 688245004138 dimer interface; other site 688245004139 active site/substrate binding site 688245004140 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245004141 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 688245004142 C-term; Region: GreA_GreB; pfam01272 688245004143 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245004144 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245004145 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004146 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 688245004147 putative effector binding pocket; other site 688245004148 putative dimerization interface; other site 688245004149 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245004150 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004151 NAD(P) binding site; other site 688245004152 active site 688245004153 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 688245004154 enoyl-CoA hydratase; Provisional; Region: PRK08138 688245004155 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 688245004156 substrate binding site; other site 688245004157 oxyanion hole (OAH) forming residues; other site 688245004158 trimer interface; other site 688245004159 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245004160 classical (c) SDRs; Region: SDR_c; cd05233 688245004161 NAD(P) binding site; other site 688245004162 active site 688245004163 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 688245004164 DUF35 OB-fold domain; Region: DUF35; pfam01796 688245004165 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245004166 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 688245004167 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004168 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and...; Region: SAV4209; cd03455 688245004169 putative active site; other site 688245004170 putative catalytic site; other site 688245004171 lipid-transfer protein; Provisional; Region: PRK07855 688245004172 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 3-ketacyl-; Region: SCP-x_thiolase; cd00829 688245004173 active site 688245004174 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245004175 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004176 active site 688245004177 long-chain-acyl-CoA synthetase; Validated; Region: PRK08279 688245004178 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004179 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245004180 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004181 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 688245004182 active site 688245004183 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 688245004184 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 688245004185 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 688245004186 active site 688245004187 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07656 688245004188 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004189 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 688245004190 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 688245004191 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 688245004192 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 688245004193 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 688245004194 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 688245004195 Ycf48-like protein; Provisional; Region: PRK13684 688245004196 thiolase; Provisional; Region: PRK06158 688245004197 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 3-ketacyl-; Region: SCP-x_thiolase; cd00829 688245004198 active site 688245004199 DUF35 OB-fold domain; Region: DUF35; pfam01796 688245004200 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 688245004201 active site 2 688245004202 active site 1 688245004203 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 688245004204 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 688245004205 N-terminal plug; other site 688245004206 ligand-binding site; other site 688245004207 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 688245004208 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 688245004209 active site 688245004210 catalytic residues; other site 688245004211 metal-binding site 688245004212 DmpG-like communication domain; Region: DmpG_comm; pfam07836 688245004213 acetaldehyde dehydrogenase; Validated; Region: PRK08300 688245004214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004215 Prokaryotic acetaldehyde dehydrogenase, dimerization; Region: AcetDehyd-dimer; pfam09290 688245004216 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245004217 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 688245004218 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; cl12031 688245004219 Flavin Reductases; Region: FlaRed; cl00801 688245004220 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245004221 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004222 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245004223 active site 688245004224 3-ketosteroid-delta-1-dehydrogenase; Reviewed; Region: PRK07843 688245004225 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004226 hypothetical protein; Validated; Region: PRK07121 688245004227 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004228 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 688245004229 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...; Region: PA_degradation_oxidoreductase_like; cd06214 688245004230 FAD binding pocket; other site 688245004231 FAD binding motif; other site 688245004232 phosphate binding motif; other site 688245004233 beta-alpha-beta structure motif; other site 688245004234 NAD(p) ribose binding residues; other site 688245004235 NAD binding pocket; other site 688245004236 NAD(P)-pyrophosphate-nicotinamide binding residues; other site 688245004237 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 688245004238 catalytic loop; other site 688245004239 iron binding site; other site 688245004240 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07656 688245004241 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004242 Protein of unknown function DUF45; Region: DUF45; cl00636 688245004243 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245004244 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245004245 Coenzyme A binding pocket; other site 688245004246 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 688245004247 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 688245004248 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 688245004249 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 688245004250 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 688245004251 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 688245004252 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 688245004253 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 688245004254 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 688245004255 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 688245004256 CrcB-like protein; Region: CRCB; cl09114 688245004257 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 688245004258 Uncharacterized protein conserved in bacteria (DUF2199); Region: DUF2199; cl02048 688245004259 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; cl12011 688245004260 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 688245004261 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245004262 Coenzyme A binding pocket; other site 688245004263 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 688245004264 Fumarase C-terminus; Region: Fumerase_C; cl00795 688245004265 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 688245004266 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 688245004267 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 688245004268 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004269 metal-binding site 688245004270 active site 688245004271 I-site; other site 688245004272 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 688245004273 fumarate hydratase; Reviewed; Region: fumC; PRK00485 688245004274 Class II fumarases; Region: Fumarase_classII; cd01362 688245004275 active site 688245004276 tetramer interface; other site 688245004277 Putative ParB-like nuclease; Region: ParBc_2; cl01772 688245004278 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 688245004279 Permease family; Region: Xan_ur_permease; cl00967 688245004280 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 688245004281 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 688245004282 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 688245004283 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 688245004284 putative substrate translocation pore; other site 688245004285 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004286 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 688245004287 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cd00216 688245004288 Trp docking motif; other site 688245004289 'Velcro' closure; other site 688245004290 active site 688245004291 Cytochrome c; Region: Cytochrom_C; cl11414 688245004292 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 688245004293 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 688245004294 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 688245004295 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 688245004296 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 688245004297 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 688245004298 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 688245004299 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 688245004300 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...; Region: TM_PBP2; cd06261 688245004301 dimer interface; other site 688245004302 conserved gate region; other site 688245004303 putative PBP binding loops; other site 688245004304 ABC-ATPase subunit interface; other site 688245004305 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 688245004306 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 688245004307 Walker A/P-loop; other site 688245004308 ATP binding site; other site 688245004309 Q-loop/lid; other site 688245004310 ABC transporter signature motif; other site 688245004311 Walker B; other site 688245004312 D-loop; other site 688245004313 H-loop/switch region; other site 688245004314 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 688245004315 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 688245004316 acetyl-CoA synthetase; Provisional; Region: PRK00174 688245004317 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 688245004318 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004319 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245004320 argininosuccinate synthase; Region: argG; TIGR00032 688245004321 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 688245004322 Ligand Binding Site; other site 688245004323 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 688245004324 Rickettsia 17 kDa surface antigen; Region: Rick_17kDa_Anti; cl10470 688245004325 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 688245004326 putative catalytic residues; other site 688245004327 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245004328 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245004329 Sporulation related domain; Region: SPOR; cl10051 688245004330 Colicin V production protein; Region: Colicin_V; cl00567 688245004331 amidophosphoribosyltransferase; Provisional; Region: PRK09246 688245004332 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 688245004333 tetramer interface; other site 688245004334 active site 688245004335 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245004336 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245004337 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 688245004338 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 688245004339 homodimer interface; other site 688245004340 substrate-cofactor binding pocket; other site 688245004341 pyridoxal 5'-phosphate binding site; other site 688245004342 catalytic residue; other site 688245004343 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 688245004344 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 688245004345 active site 688245004346 HIGH motif; other site 688245004347 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 688245004348 active site 688245004349 KMSKS motif; other site 688245004350 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 688245004351 Outer membrane efflux protein; Region: OEP; pfam02321 688245004352 Outer membrane efflux protein; Region: OEP; pfam02321 688245004353 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245004354 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 688245004355 Nitrogen regulatory protein P-II; Region: P-II; cl00412 688245004356 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245004357 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 688245004358 NAD binding site; other site 688245004359 homotetramer interface; other site 688245004360 homodimer interface; other site 688245004361 active site 688245004362 Phasin protein; Region: Phasin_2; cl11491 688245004363 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...; Region: 4HBT; cd00586 688245004364 active site 688245004365 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 688245004366 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: PncB_like; cd01401 688245004367 active site 688245004368 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; cl09110 688245004369 glyoxylate reductase; Reviewed; Region: PRK13243 688245004370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004371 macrophage migration inhibition factor-like protein; Provisional; Region: PTZ00397 688245004372 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 688245004373 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 688245004374 RmuC family; Region: RmuC; pfam02646 688245004375 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 688245004376 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245004377 putative substrate translocation pore; other site 688245004378 tetratricopeptide repeat protein; Provisional; Region: PRK11788 688245004379 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 688245004380 binding surface 688245004381 TPR motif; other site 688245004382 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 688245004383 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 higher-...; Region: HU_IHF; cd00591 688245004384 IHF dimer interface; other site 688245004385 IHF - DNA interface; other site 688245004386 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 688245004387 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 688245004388 RNA binding site; other site 688245004389 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 688245004390 RNA binding site; other site 688245004391 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 688245004392 RNA binding site; other site 688245004393 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 of...; Region: S1_RPS1_repeat_ec4; cd05689 688245004394 RNA binding site; other site 688245004395 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 of...; Region: S1_RPS1_repeat_ec5; cd05690 688245004396 RNA binding site; other site 688245004397 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 of...; Region: S1_RPS1_repeat_ec6; cd05691 688245004398 RNA binding site; other site 688245004399 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 688245004400 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 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 688245004401 hinge; other site 688245004402 active site 688245004403 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 688245004404 CMP-binding site; other site 688245004405 The sites determining sugar specificity; other site 688245004406 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 688245004407 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004408 Chorismate mutase type II; Region: CM_2; cl00693 688245004409 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 688245004410 Prephenate dehydratase; Region: PDT; pfam00800 688245004411 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 688245004412 putative L-Phe binding site; other site 688245004413 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 688245004414 pyridoxal 5'-phosphate binding pocket; other site 688245004415 catalytic residue; other site 688245004416 DNA gyrase subunit A; Validated; Region: PRK05560 688245004417 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 in...; Region: TOP4c; cd00187 688245004418 CAP-like domain; other site 688245004419 active site 688245004420 primary dimer interface; other site 688245004421 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004422 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004423 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004424 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004425 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004426 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 688245004427 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 688245004428 ligand binding site; other site 688245004429 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 688245004430 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 688245004431 S-adenosylmethionine binding site; other site 688245004432 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 688245004433 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 688245004434 motif II; other site 688245004435 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 688245004436 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 688245004437 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 688245004438 Phage integrase family; Region: Phage_integrase; pfam00589 688245004439 DNA binding site 688245004440 Int/Topo IB signature motif; other site 688245004441 active site 688245004442 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004443 metal-binding site 688245004444 active site 688245004445 I-site; other site 688245004446 Putative exonuclease, RdgC; Region: RdgC; cl01122 688245004447 Sensors of blue-light using FAD; Region: BLUF; pfam04940 688245004448 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245004449 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 688245004450 non-specific DNA binding site; other site 688245004451 salt bridge; other site 688245004452 sequence-specific DNA binding site; other site 688245004453 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 688245004454 Poly(A) polymerase [RNA processing and modification]; Region: PAP1; COG5186 688245004455 Gas vesicle protein G; Region: GvpG; pfam05120 688245004456 Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked...; Region: Ntn_Asparaginase_2_like; cl00635 688245004457 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 688245004458 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl01450 688245004459 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 688245004460 active site 688245004461 phosphorylation site 688245004462 intermolecular recognition site; other site 688245004463 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...; Region: LuxR_C_like; cd06170 688245004464 DNA binding residues 688245004465 dimerization interface; other site 688245004466 integrase; Provisional; Region: PRK09692 688245004467 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 688245004468 Int/Topo IB signature motif; other site 688245004469 active site 688245004470 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...; Region: FNR_like; cl06868 688245004471 FAD binding pocket; other site 688245004472 phosphate binding motif; other site 688245004473 beta-alpha-beta structure motif; other site 688245004474 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...; Region: gram_neg_porins; cd00342 688245004475 trimer interface; other site 688245004476 eyelet of channel; other site 688245004477 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 688245004478 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 688245004479 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 688245004480 Transposase DDE domain; Region: Transposase_11; pfam01609 688245004481 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 688245004482 Integrase core domain; Region: rve; cl01316 688245004483 cation-binding hemerythrin HHE family protein; Provisional; Region: PRK01917 688245004484 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 688245004485 octamerization interface; other site 688245004486 diferric-oxygen binding site; other site 688245004487 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245004488 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...; Region: PDR_like; cd06185 688245004489 FMN-binding pocket; other site 688245004490 flavin binding motif; other site 688245004491 phosphate binding motif; other site 688245004492 beta-alpha-beta structure motif; other site 688245004493 NAD binding pocket; other site 688245004494 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 688245004495 catalytic loop; other site 688245004496 iron binding site; other site 688245004497 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 688245004498 d-galactonate transporter; Region: 2A0114; TIGR00893 688245004499 putative substrate translocation pore; other site 688245004500 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 688245004501 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 688245004502 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245004503 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004505 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 688245004506 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 3,4-...; Region: Rieske_RO_Alpha_PhDO_like; cd03479 688245004507 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 688245004508 hydrophobic ligand binding site; other site 688245004509 putative transposase OrfB; Reviewed; Region: PHA02517 688245004510 Integrase core domain; Region: rve; cl01316 688245004511 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 688245004512 Transposase; Region: Transposase_9; pfam01548 688245004513 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 688245004514 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 688245004515 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004516 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245004517 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 688245004518 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)...; Region: Rieske; cl00938 688245004519 iron-sulfur cluster; other site 688245004520 [2Fe-2S] cluster binding site; other site 688245004521 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 688245004522 putative alpha subunit interface; other site 688245004523 putative active site; other site 688245004524 putative substrate binding site; other site 688245004525 Fe binding site; other site 688245004526 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 688245004527 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 688245004528 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 688245004529 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 688245004530 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 688245004531 catalytic loop; other site 688245004532 iron binding site; other site 688245004533 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...; Region: flavin_oxioreductase; cd06189 688245004534 FAD binding pocket; other site 688245004535 FAD binding motif; other site 688245004536 phosphate binding motif; other site 688245004537 beta-alpha-beta structure motif; other site 688245004538 NAD binding pocket; other site 688245004539 potential frameshift: common BLAST hit: gi|76810996|ref|YP_333177.1| integrase core subunit 688245004540 Integrase core domain; Region: rve; cl01316 688245004541 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 688245004542 non-specific DNA binding site; other site 688245004543 salt bridge; other site 688245004544 sequence-specific DNA binding site; other site 688245004545 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 688245004546 Domain of unknown function (DUF932); Region: DUF932; cl12129 688245004547 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 688245004548 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 688245004549 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 688245004550 HsdM N-terminal domain; Region: HsdM_N; pfam12161 688245004551 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 688245004552 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; cl12011 688245004553 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 688245004554 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 688245004555 active site 688245004556 phosphorylation site 688245004557 intermolecular recognition site; other site 688245004558 dimerization interface; other site 688245004559 hypothetical protein; Provisional; Region: PRK13560 688245004560 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 688245004561 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004562 metal-binding site 688245004563 active site 688245004564 I-site; other site 688245004565 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 688245004566 CHASE domain; Region: CHASE; cl01369 688245004567 PAS domain S-box; Region: sensory_box; TIGR00229 688245004568 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 688245004569 hypothetical protein; Provisional; Region: PRK13560 688245004570 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 688245004571 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 688245004572 putative active site; other site 688245004573 heme pocket; other site 688245004574 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 688245004575 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 trans-...; Region: HisKA; cd00082 688245004576 dimer interface; other site 688245004577 phosphorylation site 688245004578 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 688245004579 ATP binding site; other site 688245004580 Mg2+ binding site; other site 688245004581 G-X-G motif; other site 688245004582 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 688245004583 active site 688245004584 phosphorylation site 688245004585 intermolecular recognition site; other site 688245004586 dimerization interface; other site 688245004587 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 688245004588 active site 688245004589 phosphorylation site 688245004590 intermolecular recognition site; other site 688245004591 dimerization interface; other site 688245004592 Transposase DDE domain; Region: Transposase_11; pfam01609 688245004593 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 688245004594 Transposase; Region: Transposase_9; pfam01548 688245004595 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 688245004596 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 688245004597 Transposase DDE domain; Region: Transposase_11; pfam01609 688245004598 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 688245004599 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245004600 CHASE domain; Region: CHASE; cl01369 688245004601 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 688245004602 putative active site; other site 688245004603 PAS fold; Region: PAS_3; pfam08447 688245004604 heme pocket; other site 688245004605 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004606 metal-binding site 688245004607 active site 688245004608 I-site; other site 688245004609 potential frameshift: common BLAST hit: gi|110639316|ref|YP_679525.1| restriction/modification methyltransferase 688245004610 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 688245004611 HsdM N-terminal domain; Region: HsdM_N; pfam12161 688245004612 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; cl12011 688245004613 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 688245004614 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 688245004615 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 688245004616 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 688245004617 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl01057 688245004618 Transposase DDE domain; Region: Transposase_11; pfam01609 688245004619 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 688245004620 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 688245004621 Phage integrase family; Region: Phage_integrase; pfam00589 688245004622 DNA binding site 688245004623 Int/Topo IB signature motif; other site 688245004624 active site 688245004625 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; cl12011 688245004626 Putative exonuclease, RdgC; Region: RdgC; cl01122 688245004627 Sensors of blue-light using FAD; Region: BLUF; pfam04940 688245004628 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245004629 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...; Region: AAA; cd00009 688245004630 Walker A motif; other site 688245004631 ATP binding site; other site 688245004632 Walker B motif; other site 688245004633 arginine finger; other site 688245004634 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 688245004635 active site 688245004636 Zn-binding site; other site 688245004637 helicase 45; Provisional; Region: PTZ00424 688245004638 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 688245004639 ATP binding site; other site 688245004640 Mg++ binding site; other site 688245004641 motif III; other site 688245004642 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 688245004643 nucleotide binding region; other site 688245004644 ATP-binding site; other site 688245004645 Transcriptional regulatory protein LGE1; Region: Lge1; pfam11488 688245004646 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 688245004647 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245004648 Walker A/P-loop; other site 688245004649 ATP binding site; other site 688245004650 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245004651 Q-loop/lid; other site 688245004652 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245004653 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245004654 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 688245004655 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly...; Region: nylC_like; cd02252 688245004656 putative active site pocket; other site 688245004657 cleavage site 688245004658 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 688245004659 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 688245004660 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 688245004661 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 688245004662 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 688245004663 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 688245004664 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 688245004665 Protein of unknown function, DUF; Region: DUF411; cl01142 688245004666 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 688245004667 Multicopper oxidase; Region: Cu-oxidase; cl14658 688245004668 Multicopper oxidase; Region: Cu-oxidase; cl14658 688245004669 Outer membrane efflux protein; Region: OEP; pfam02321 688245004670 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 688245004671 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245004672 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; cl11391 688245004673 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 688245004674 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 688245004675 DNA binding residues 688245004676 dimer interface; other site 688245004677 putative metal binding site; other site 688245004678 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 688245004679 mce related protein; Region: MCE; cl03606 688245004680 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...; Region: gram_neg_porins; cd00342 688245004681 trimer interface; other site 688245004682 eyelet of channel; other site 688245004683 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...; Region: TM_ABC_iron-siderophores_like; cd06550 688245004684 ABC-ATPase subunit interface; other site 688245004685 dimer interface; other site 688245004686 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...; Region: TM_ABC_iron-siderophores_like; cl00462 688245004687 dimer interface; other site 688245004688 putative PBP binding regions; other site 688245004689 ABC-ATPase subunit interface; other site 688245004690 iron-enterobactin transporter periplasmic binding protein; Provisional; Region: PRK10957 688245004691 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...; Region: TroA-like; cl00262 688245004692 intersubunit interface; other site 688245004693 iron-enterobactin transporter ATP-binding protein; Provisional; Region: PRK10253 688245004694 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245004695 Walker A/P-loop; other site 688245004696 ATP binding site; other site 688245004697 Q-loop/lid; other site 688245004698 ABC transporter signature motif; other site 688245004699 Walker B; other site 688245004700 D-loop; other site 688245004701 H-loop/switch region; other site 688245004702 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004703 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245004704 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245004705 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245004706 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 688245004707 N-terminal plug; other site 688245004708 ligand-binding site; other site 688245004709 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 688245004710 active site 688245004711 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 688245004712 non-prolyl cis peptide bond; other site 688245004713 Protein of unknown function (DUF454); Region: DUF454; cl01063 688245004714 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 688245004715 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 688245004716 substrate binding site; other site 688245004717 oxyanion hole (OAH) forming residues; other site 688245004718 trimer interface; other site 688245004719 Protein of unknown function DUF72; Region: DUF72; cl00777 688245004720 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 688245004721 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...; Region: S1_Tex; cd05685 688245004722 RNA binding site; other site 688245004723 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 688245004724 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245004725 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245004726 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; cl09944 688245004727 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...; Region: LuxR_C_like; cd06170 688245004728 DNA binding residues 688245004729 dimerization interface; other site 688245004730 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 688245004731 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 688245004732 ATP binding site; other site 688245004733 Mg2+ binding site; other site 688245004734 G-X-G motif; other site 688245004735 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 688245004736 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 688245004737 Domain of unknown function DUF20; Region: UPF0118; cl00465 688245004738 Domain of unknown function DUF20; Region: UPF0118; cl00465 688245004739 GAF domain; Region: GAF; cl00853 688245004740 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 688245004741 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 688245004742 putative active site; other site 688245004743 metal-binding site 688245004744 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...; Region: gram_neg_porins; cd00342 688245004745 trimer interface; other site 688245004746 eyelet of channel; other site 688245004747 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_5; cd07823 688245004748 putative hydrophobic ligand binding site; other site 688245004749 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245004750 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245004751 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 688245004752 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 688245004753 4-hydroxybenzoyl-CoA reductase, alpha subunit; Region: 4hydrxCoA_A; TIGR03194 688245004754 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 688245004755 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245004756 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 688245004757 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245004758 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004759 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245004760 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245004761 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245004762 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245004763 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 688245004764 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 688245004765 N-terminal plug; other site 688245004766 ligand-binding site; other site 688245004767 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 688245004768 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 688245004769 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245004770 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; cl12031 688245004771 substrate binding pocket; other site 688245004772 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 688245004773 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...; Region: 4HBT; cd00586 688245004774 active site 688245004775 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245004776 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 688245004777 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 688245004778 YceG-like family; Region: YceG; pfam02618 688245004779 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 688245004780 dimerization interface; other site 688245004781 thymidylate kinase; Validated; Region: tmk; PRK00698 688245004782 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...; Region: TMPK; cd01672 688245004783 TMP-binding site; other site 688245004784 ATP-binding site; other site 688245004785 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 688245004786 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245004787 PilZ domain; Region: PilZ; cl01260 688245004788 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 688245004789 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 688245004790 active site 688245004791 ankyrin repeat protein; Provisional; Region: PHA03100 688245004792 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 688245004793 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 688245004794 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245004795 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 688245004796 Walker A/P-loop; other site 688245004797 ATP binding site; other site 688245004798 Q-loop/lid; other site 688245004799 ABC transporter signature motif; other site 688245004800 Walker B; other site 688245004801 D-loop; other site 688245004802 H-loop/switch region; other site 688245004803 translocation protein TolB; Provisional; Region: tolB; PRK02889 688245004804 TolB amino-terminal domain; Region: TolB_N; pfam04052 688245004805 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 688245004806 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 688245004807 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 688245004808 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 688245004809 ligand binding site; other site 688245004810 HemX; Region: HemX; cl14667 688245004811 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 688245004812 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 688245004813 binding surface 688245004814 TPR motif; other site 688245004815 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 688245004816 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin...; Region: YgdL_like; cd00755 688245004817 putative ATP binding site; other site 688245004818 putative substrate interface; other site 688245004819 Cytochrome c; Region: Cytochrom_C; cl11414 688245004820 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 688245004821 dinuclear metal binding motif; other site 688245004822 RNA polymerase sigma factor; Provisional; Region: PRK11922 688245004823 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245004824 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...; Region: Sigma70_r4; cd06171 688245004825 DNA binding residues 688245004826 GAF domain; Region: GAF; cl00853 688245004827 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 688245004828 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245004829 DNA binding residues 688245004830 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 688245004831 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 688245004832 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 688245004833 FeS/SAM binding site; other site 688245004834 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14951 688245004835 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...; Region: AAA; cd00009 688245004836 Walker A motif; other site 688245004837 ATP binding site; other site 688245004838 Walker B motif; other site 688245004839 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245004840 arginine finger; other site 688245004841 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 688245004842 Uncharacterized BCR, YbaB family COG0718; Region: DUF149; cl00494 688245004843 recombination protein RecR; Reviewed; Region: recR; PRK00076 688245004844 RecR protein; Region: RecR; pfam02132 688245004845 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 688245004846 putative active site; other site 688245004847 putative metal-binding site; other site 688245004848 tetramer interface; other site 688245004849 MLTD_N; Region: MLTD_N; pfam06474 688245004850 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 catalyze...; Region: LT_GEWL; cd00254 688245004851 N-acetyl-D-glucosamine binding site; other site 688245004852 catalytic residue; other site 688245004853 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 688245004854 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 688245004855 putative peptidoglycan binding site; other site 688245004856 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245004857 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; cl12011 688245004858 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 688245004859 RNA/DNA hybrid binding site; other site 688245004860 active site 688245004861 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 688245004862 catalytic residues; other site 688245004863 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 688245004864 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 688245004865 dimer interface; other site 688245004866 putative functional site; other site 688245004867 putative MPT binding site; other site 688245004868 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 688245004869 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 688245004870 GTP binding site; other site 688245004871 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 688245004872 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 688245004873 FeS/SAM binding site; other site 688245004874 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 688245004875 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 688245004876 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245004877 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 688245004878 ligand binding site; other site 688245004879 flexible hinge region; other site 688245004880 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004881 Protein of unknown function (DUF962); Region: DUF962; cl01879 688245004882 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 688245004883 dimer interface; other site 688245004884 substrate binding site; other site 688245004885 metal binding sites; metal-binding site 688245004886 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 688245004887 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245004888 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245004889 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245004890 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245004891 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245004892 FemAB family; Region: FemAB; cl11444 688245004893 Protein of unknown function, DUF482; Region: DUF482; pfam04339 688245004894 NAD synthetase; Provisional; Region: PRK13981 688245004895 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 688245004896 multimer interface; other site 688245004897 active site 688245004898 catalytic triad; other site 688245004899 protein interface 1; other site 688245004900 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...; Region: NAD_synthase; cd00553 688245004901 homodimer interface; other site 688245004902 NAD binding pocket; other site 688245004903 ATP binding pocket; other site 688245004904 Mg binding site; other site 688245004905 active-site loop 688245004906 Nitrogen regulatory protein P-II; Region: P-II; cl00412 688245004907 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 688245004908 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 688245004909 RDD family; Region: RDD; cl00746 688245004910 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 688245004911 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 688245004912 RNA polymerase factor sigma-70; Validated; Region: PRK09047 688245004913 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...; Region: Sigma70_r4; cd06171 688245004914 DNA binding residues 688245004915 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 688245004916 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 688245004917 PYR/PP interface; other site 688245004918 dimer interface; other site 688245004919 TPP binding site; other site 688245004920 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 688245004921 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 688245004922 TPP-binding site; other site 688245004923 dimer interface; other site 688245004924 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 688245004925 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 688245004926 putative valine binding site; other site 688245004927 dimer interface; other site 688245004928 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 688245004929 ketol-acid reductoisomerase; Provisional; Region: PRK05479 688245004930 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245004931 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 688245004932 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 688245004933 2-isopropylmalate synthase; Validated; Region: PRK03739 688245004934 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 688245004935 active site 688245004936 catalytic residues; other site 688245004937 metal-binding site 688245004938 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 688245004939 2-isopropylmalate synthase; Validated; Region: PRK00915 688245004940 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 688245004941 active site 688245004942 catalytic residues; other site 688245004943 metal-binding site 688245004944 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 688245004945 Beta-lactamase; Region: Beta-lactamase; cl01009 688245004946 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 688245004947 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245004948 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245004949 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245004950 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 688245004951 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 688245004952 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 688245004953 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 688245004954 elongation factor P; Validated; Region: PRK00529 688245004955 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 688245004956 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 688245004957 RNA binding site; other site 688245004958 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 688245004959 RNA binding site; other site 688245004960 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 688245004961 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245004962 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 688245004963 putative dimerization interface; other site 688245004964 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245004965 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 688245004966 active site 688245004967 catalytic residues; other site 688245004968 metal-binding site 688245004969 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 688245004970 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 688245004971 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 688245004972 UvrB/uvrC motif; Region: UVR; pfam02151 688245004973 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 688245004974 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 688245004975 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 higher-...; Region: HU_IHF; cd00591 688245004976 IHF dimer interface; other site 688245004977 IHF - DNA interface; other site 688245004978 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245004979 metal-binding site 688245004980 active site 688245004981 I-site; other site 688245004982 Putative exonuclease, RdgC; Region: RdgC; cl01122 688245004983 periplasmic folding chaperone; Provisional; Region: PRK10788 688245004984 PPIC-type PPIASE domain; Region: Rotamase; cl08278 688245004985 Protein of unknown function (DUF1641); Region: DUF1641; cl01025 688245004986 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 688245004987 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245004988 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245004989 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 688245004990 rRNA binding site; other site 688245004991 predicted 30S ribosome binding site; other site 688245004992 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 688245004993 PII uridylyl-transferase; Provisional; Region: PRK03059 688245004994 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 688245004995 metal binding triad; other site 688245004996 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 688245004997 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245004998 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 688245004999 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 688245005000 methionine aminopeptidase; Reviewed; Region: PRK07281 688245005001 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 688245005002 active site 688245005003 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 688245005004 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 688245005005 dimerization interface; other site 688245005006 ATP binding site; other site 688245005007 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 688245005008 dimerization interface; other site 688245005009 ATP binding site; other site 688245005010 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 688245005011 putative active site; other site 688245005012 catalytic triad; other site 688245005013 SWIM zinc finger; Region: SWIM; cl11618 688245005014 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 688245005015 VWA YIEM type: 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-...; Region: VWA_YIEM_type; cd01462 688245005016 metal ion-dependent adhesion site (MIDAS); other site 688245005017 Protein of unknown function (DUF808); Region: DUF808; cl01002 688245005018 Surface antigen; Region: Surface_Ag_2; cl01155 688245005019 probable methyltransferase; Region: TIGR03438 688245005020 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 688245005021 conserved hypothetical protein TIGR03440; Region: unchr_TIGR03440 688245005022 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 688245005023 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 688245005024 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 688245005025 homodimer interface; other site 688245005026 substrate-cofactor binding pocket; other site 688245005027 pyridoxal 5'-phosphate binding site; other site 688245005028 catalytic residue; other site 688245005029 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005030 metal-binding site 688245005031 active site 688245005032 I-site; other site 688245005033 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245005034 active site 688245005035 enoyl-CoA hydratase; Provisional; Region: PRK06688 688245005036 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 688245005037 substrate binding site; other site 688245005038 oxyanion hole (OAH) forming residues; other site 688245005039 trimer interface; other site 688245005040 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 688245005041 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245005042 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245005043 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245005044 active site 688245005045 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245005046 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005047 NAD(P) binding site; other site 688245005048 active site 688245005049 SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid...; Region: SAV4209_like; cd03453 688245005050 active site 688245005051 catalytic site; other site 688245005052 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 688245005053 active site 688245005054 catalytic site; other site 688245005055 lipid-transfer protein; Provisional; Region: PRK08256 688245005056 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 3-ketacyl-; Region: SCP-x_thiolase; cd00829 688245005057 active site 688245005058 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245005059 SurA N-terminal domain; Region: SurA_N; pfam09312 688245005060 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245005061 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245005062 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005063 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245005064 NAD(P) binding site; other site 688245005065 active site 688245005066 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 688245005067 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245005068 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245005069 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245005070 active site 688245005071 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 688245005072 enoyl-CoA hydratase; Provisional; Region: PRK07827 688245005073 substrate binding site; other site 688245005074 oxyanion hole (OAH) forming residues; other site 688245005075 trimer interface; other site 688245005076 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 688245005077 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245005078 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245005079 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245005080 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 688245005081 carboxyltransferase (CT) interaction site; other site 688245005082 biotinylation site; other site 688245005083 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245005084 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245005085 active site 688245005086 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245005087 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07656 688245005088 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245005089 short chain dehydrogenase; Provisional; Region: PRK07576 688245005090 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 688245005091 NAD(P) binding site; other site 688245005092 substrate binding site; other site 688245005093 homotetramer interface; other site 688245005094 active site 688245005095 homodimer interface; other site 688245005096 acyl-CoA synthetase; Validated; Region: PRK08316 688245005097 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245005098 hypothetical protein; Provisional; Region: PRK06194 688245005099 classical (c) SDRs; Region: SDR_c; cd05233 688245005100 NAD(P) binding site; other site 688245005101 active site 688245005102 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245005103 classical (c) SDRs; Region: SDR_c; cd05233 688245005104 NAD(P) binding site; other site 688245005105 active site 688245005106 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 688245005107 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005108 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; cl12031 688245005109 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 688245005110 substrate binding pocket; other site 688245005111 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 688245005112 Peptidase family U32; Region: Peptidase_U32; cl03113 688245005113 Collagenase; Region: DUF3656; pfam12392 688245005114 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...; Region: Nudix_Hydrolase; cd02883 688245005115 nudix motif; other site 688245005116 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...; Region: Nudix_Hydrolase; cl00447 688245005117 RNA 2'-phosphotransferase, Tpt1 / KptA family; Region: PTS_2-RNA; cl00804 688245005118 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); Region: NT5C; cl01869 688245005119 Domain of unknown function (DUF1768); Region: DUF1768; cl01271 688245005120 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 688245005121 potential protein location (hypothetical protein) that overlaps protein (methyl-accepting chemotaxis protein) 688245005122 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245005123 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 688245005124 dimerization interface; other site 688245005125 ligand binding site; other site 688245005126 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 688245005127 nucleoside/Zn binding site; other site 688245005128 dimer interface; other site 688245005129 catalytic motif; other site 688245005130 haloalkane dehalogenase; Provisional; Region: PRK00870 688245005131 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 688245005132 dimer interface; other site 688245005133 catalytic triad; other site 688245005134 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 688245005135 elongation factor G; Reviewed; Region: PRK00007 688245005136 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 688245005137 G1 box; other site 688245005138 putative GEF interaction site; other site 688245005139 GTP/Mg2+ binding site; other site 688245005140 Switch I region; other site 688245005141 G2 box; other site 688245005142 G3 box; other site 688245005143 Switch II region; other site 688245005144 G4 box; other site 688245005145 G5 box; other site 688245005146 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...; Region: EFG_mtEFG_II; cd04088 688245005147 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...; Region: EFG_mtEFG1_IV; cd01434 688245005148 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...; Region: EFG_mtEFG_C; cd03713 688245005149 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 688245005150 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 7...; Region: Ntn_PGA_like; cd03747 688245005151 active site 688245005152 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; cl12031 688245005153 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245005154 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; cl12031 688245005155 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...; Region: Aldo_ket_red; cd06660 688245005156 active site 688245005157 catalytic tetrad; other site 688245005158 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 688245005159 putative deacylase active site; other site 688245005160 Domain of unknown function (DUF205); Region: DUF205; cl00410 688245005161 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 688245005162 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; cl12011 688245005163 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]; Region: COG4262 688245005164 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 688245005165 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 688245005166 catalytic motif; other site 688245005167 Catalytic residue; other site 688245005168 Protein of unknown function (DUF520); Region: DUF520; cl00723 688245005169 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 688245005170 FAD binding domain; Region: FAD_binding_4; pfam01565 688245005171 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 688245005172 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 688245005173 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 688245005174 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 688245005175 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 688245005176 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 688245005177 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005178 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245005179 NAD(P) binding site; other site 688245005180 active site 688245005181 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 688245005182 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245005183 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245005184 Sel1 repeat; Region: Sel1; cl02723 688245005185 Sel1 repeat; Region: Sel1; cl02723 688245005186 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 688245005187 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245005188 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 688245005189 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 688245005190 Protein export membrane protein; Region: SecD_SecF; cl14618 688245005191 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 688245005192 Outer membrane efflux protein; Region: OEP; pfam02321 688245005193 Outer membrane efflux protein; Region: OEP; pfam02321 688245005194 RNA polymerase sigma factor; Provisional; Region: PRK12528 688245005195 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245005196 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...; Region: Sigma70_r4; cd06171 688245005197 DNA binding residues 688245005198 fec operon regulator FecR; Reviewed; Region: PRK09774 688245005199 FecR protein; Region: FecR; pfam04773 688245005200 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245005201 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 688245005202 N-terminal plug; other site 688245005203 ligand-binding site; other site 688245005204 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 688245005205 NfeD-like; Region: NfeD; cl00686 688245005206 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; cl09944 688245005207 lysine decarboxylase LdcC; Provisional; Region: PRK15399 688245005208 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 688245005209 pyridoxal 5'-phosphate binding pocket; other site 688245005210 catalytic residue; other site 688245005211 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 688245005212 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 688245005213 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245005214 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 688245005215 active site 688245005216 catalytic residues; other site 688245005217 metal-binding site 688245005218 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005219 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245005220 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245005221 DNA ligase; Provisional; Region: PRK09125 688245005222 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 688245005223 DNA binding site 688245005224 active site 688245005225 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 688245005226 DNA binding site 688245005227 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 688245005228 E-class dimer interface; other site 688245005229 P-class dimer interface; other site 688245005230 active site 688245005231 Cu2+ binding site; other site 688245005232 Zn2+ binding site; other site 688245005233 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 688245005234 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 688245005235 NAD binding site; other site 688245005236 homotetramer interface; other site 688245005237 homodimer interface; other site 688245005238 substrate binding site; other site 688245005239 active site 688245005240 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 688245005241 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 688245005242 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...; Region: TM_PBP2; cd06261 688245005243 dimer interface; other site 688245005244 conserved gate region; other site 688245005245 ABC-ATPase subunit interface; other site 688245005246 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...; Region: TM_PBP2; cd06261 688245005247 dimer interface; other site 688245005248 conserved gate region; other site 688245005249 putative PBP binding loops; other site 688245005250 ABC-ATPase subunit interface; other site 688245005251 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 688245005252 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245005253 Walker A/P-loop; other site 688245005254 ATP binding site; other site 688245005255 Q-loop/lid; other site 688245005256 ABC transporter signature motif; other site 688245005257 Walker B; other site 688245005258 D-loop; other site 688245005259 H-loop/switch region; other site 688245005260 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 688245005261 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245005262 Walker A/P-loop; other site 688245005263 ATP binding site; other site 688245005264 Q-loop/lid; other site 688245005265 ABC transporter signature motif; other site 688245005266 Walker B; other site 688245005267 D-loop; other site 688245005268 H-loop/switch region; other site 688245005269 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 688245005270 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...; Region: DnaJ; cd06257 688245005271 HSP70 interaction site; other site 688245005272 DnaJ C terminal region; Region: DnaJ_C; pfam01556 688245005273 DnaJ C terminal region; Region: DnaJ_C; pfam01556 688245005274 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 688245005275 catalytic residues; other site 688245005276 ribosome maturation protein RimP; Reviewed; Region: PRK00092 688245005277 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 688245005278 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 688245005279 Sm1 motif; other site 688245005280 RNA binding pocket; other site 688245005281 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 688245005282 NusA N-terminal domain; Region: NusA_N; pfam08529 688245005283 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...; Region: S1_NusA; cd04455 688245005284 RNA binding site; other site 688245005285 homodimer interface; other site 688245005286 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 688245005287 G-X-X-G motif; other site 688245005288 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 688245005289 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 688245005290 translation initiation factor IF-2; Validated; Region: infB; PRK05306 688245005291 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 688245005292 translation initiation factor IF-2; Region: IF-2; TIGR00487 688245005293 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 688245005294 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 688245005295 G1 box; other site 688245005296 putative GEF interaction site; other site 688245005297 GTP/Mg2+ binding site; other site 688245005298 Switch I region; other site 688245005299 G2 box; other site 688245005300 G3 box; other site 688245005301 Switch II region; other site 688245005302 G4 box; other site 688245005303 G5 box; other site 688245005304 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...; Region: IF2_mtIF2_II; cd03702 688245005305 Translation-initiation factor 2; Region: IF-2; pfam11987 688245005306 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...; Region: mtIF2_IVc; cd03692 688245005307 Ribosome-binding factor A; Region: RBFA; cl00542 688245005308 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 688245005309 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 688245005310 RNA binding site; other site 688245005311 active site 688245005312 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 688245005313 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 688245005314 G1 box; other site 688245005315 putative GEF interaction site; other site 688245005316 GTP/Mg2+ binding site; other site 688245005317 Switch I region; other site 688245005318 G2 box; other site 688245005319 G3 box; other site 688245005320 Switch II region; other site 688245005321 G4 box; other site 688245005322 G5 box; other site 688245005323 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 688245005324 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...; Region: BipA_TypA_C; cd03710 688245005325 Cytochrome c; Region: Cytochrom_C; cl11414 688245005326 Dehydratase family; Region: ILVD_EDD; cl00340 688245005327 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 688245005328 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 688245005329 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 688245005330 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 688245005331 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 688245005332 malonyl-CoA synthase; Validated; Region: PRK07514 688245005333 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245005334 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 688245005335 Ligand Binding Site; other site 688245005336 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 688245005337 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 688245005338 metal-binding site 688245005339 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245005340 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; cl11391 688245005341 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 688245005342 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...; Region: cbb3_Oxidase_I; cd01661 688245005343 Putative water exit pathway; other site 688245005344 Binuclear center (active site); other site 688245005345 Putative proton exit pathway; other site 688245005346 Low-spin heme binding site; other site 688245005347 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 688245005348 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of...; Region: cbb3_Oxidase_CcoQ; cl00282 688245005349 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 688245005350 Cytochrome c; Region: Cytochrom_C; cl11414 688245005351 Cytochrome c; Region: Cytochrom_C; cl11414 688245005352 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 688245005353 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 688245005354 FixH; Region: FixH; cl01254 688245005355 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 688245005356 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 688245005357 ligand binding site; other site 688245005358 flexible hinge region; other site 688245005359 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 688245005360 putative switch regulator; other site 688245005361 non-specific DNA interactions; other site 688245005362 DNA binding site 688245005363 sequence specific DNA binding site; other site 688245005364 putative cAMP binding site; other site 688245005365 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 688245005366 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 688245005367 FeS/SAM binding site; other site 688245005368 HemN C-terminal region; Region: HemN_C; pfam06969 688245005369 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 688245005370 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 688245005371 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245005372 Zn2+ binding site; other site 688245005373 Mg2+ binding site; other site 688245005374 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 688245005375 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 688245005376 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 688245005377 putative active site; other site 688245005378 heme pocket; other site 688245005379 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005380 metal-binding site 688245005381 active site 688245005382 I-site; other site 688245005383 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 688245005384 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...; Region: LuxR_C_like; cd06170 688245005385 DNA binding residues 688245005386 dimerization interface; other site 688245005387 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245005388 classical (c) SDRs; Region: SDR_c; cd05233 688245005389 NAD(P) binding site; other site 688245005390 active site 688245005391 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 688245005392 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 688245005393 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005394 metal-binding site 688245005395 active site 688245005396 I-site; other site 688245005397 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005398 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005399 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 688245005400 putative dimerization interface; other site 688245005401 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 688245005402 conserved cys residue; other site 688245005403 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245005404 aspartate racemase; Region: asp_race; TIGR00035 688245005405 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 688245005406 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 688245005407 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245005408 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005409 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...; Region: PDR_like; cd06185 688245005410 beta-alpha-beta structure motif; other site 688245005411 NAD binding pocket; other site 688245005412 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 688245005413 catalytic loop; other site 688245005414 iron binding site; other site 688245005415 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 688245005416 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)...; Region: Rieske; cl00938 688245005417 iron-sulfur cluster; other site 688245005418 [2Fe-2S] cluster binding site; other site 688245005419 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 688245005420 alpha subunit interface; other site 688245005421 active site 688245005422 substrate binding site; other site 688245005423 Fe binding site; other site 688245005424 benzoate transport; Region: 2A0115; TIGR00895 688245005425 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 688245005426 putative substrate translocation pore; other site 688245005427 Staphylococcal nuclease homologues; Region: SNc; smart00318 688245005428 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 688245005429 Catalytic site; other site 688245005430 Cell division protein ZapA; Region: ZapA; cl01146 688245005431 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 688245005432 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 688245005433 N-terminal plug; other site 688245005434 ligand-binding site; other site 688245005435 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 688245005436 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245005437 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 688245005438 catalytic triad; other site 688245005439 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 688245005440 homotrimer interface; other site 688245005441 Walker A motif; other site 688245005442 GTP binding site; other site 688245005443 Walker B motif; other site 688245005444 Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: YvrC; cd01143 688245005445 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 688245005446 putative binding site residues; other site 688245005447 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...; Region: TM_ABC_iron-siderophores_like; cl00462 688245005448 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...; Region: TM_ABC_iron-siderophores_like; cl00462 688245005449 putative PBP binding regions; other site 688245005450 ABC-ATPase subunit interface; other site 688245005451 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 688245005452 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245005453 Walker A/P-loop; other site 688245005454 ATP binding site; other site 688245005455 Q-loop/lid; other site 688245005456 ABC transporter signature motif; other site 688245005457 Walker B; other site 688245005458 D-loop; other site 688245005459 H-loop/switch region; other site 688245005460 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...; Region: CobA_CobO_BtuR; cd00561 688245005461 homodimer interface; other site 688245005462 Walker A motif; other site 688245005463 ATP binding site; other site 688245005464 hydroxycobalamin binding site; other site 688245005465 Walker B motif; other site 688245005466 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD...; Region: BluB; cd02145 688245005467 putative FMN binding site; other site 688245005468 CobD/Cbib protein; Region: CobD_Cbib; cl00561 688245005469 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 688245005470 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 688245005471 pyridoxal 5'-phosphate binding pocket; other site 688245005472 catalytic residue; other site 688245005473 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 688245005474 Cobyric acid synthase [Coenzyme metabolism]; Region: CobQ; COG1492 688245005475 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245005476 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 688245005477 catalytic triad; other site 688245005478 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 688245005479 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 688245005480 putative dimer interface; other site 688245005481 active site pocket 688245005482 putative cataytic base; other site 688245005483 endonuclease III; Provisional; Region: PRK10702 688245005484 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 688245005485 minor groove reading motif; other site 688245005486 helix-hairpin-helix signature motif; other site 688245005487 substrate binding pocket; other site 688245005488 active site 688245005489 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 688245005490 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245005491 methionine aminotransferase; Validated; Region: PRK09082 688245005492 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 688245005493 pyridoxal 5'-phosphate binding site; other site 688245005494 homodimer interface; other site 688245005495 catalytic residue; other site 688245005496 SlyX; Region: SlyX; cl01090 688245005497 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 688245005498 amidohydrolase; Region: amidohydrolases; TIGR01891 688245005499 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245005500 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 688245005501 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...; Region: PBPb; cd00134 688245005502 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245005503 substrate binding pocket; other site 688245005504 membrane-bound complex binding site; other site 688245005505 hinge residues; other site 688245005506 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...; Region: TM_PBP2; cd06261 688245005507 dimer interface; other site 688245005508 conserved gate region; other site 688245005509 putative PBP binding loops; other site 688245005510 ABC-ATPase subunit interface; other site 688245005511 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...; Region: TM_PBP2; cd06261 688245005512 dimer interface; other site 688245005513 conserved gate region; other site 688245005514 putative PBP binding loops; other site 688245005515 ABC-ATPase subunit interface; other site 688245005516 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005517 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005518 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 688245005519 dimerization interface; other site 688245005520 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245005521 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245005522 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245005523 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; cl12011 688245005524 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 688245005525 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 688245005526 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245005527 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245005528 Precorrin-8X methylmutase; Region: CbiC; cl00913 688245005529 precorrin-3B synthase; Region: CobG; TIGR02435 688245005530 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 688245005531 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 688245005532 metal ion-dependent adhesion site (MIDAS); other site 688245005533 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...; Region: AAA; cd00009 688245005534 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 688245005535 Walker A motif; other site 688245005536 ATP binding site; other site 688245005537 Walker B motif; other site 688245005538 arginine finger; other site 688245005539 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 688245005540 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 688245005541 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245005542 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 688245005543 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...; Region: CbiX_SirB_N; cd03416 688245005544 putative active site; other site 688245005545 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 688245005546 dimer interface; other site 688245005547 [2Fe-2S] cluster binding site; other site 688245005548 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 688245005549 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245005550 Walker A/P-loop; other site 688245005551 ATP binding site; other site 688245005552 Q-loop/lid; other site 688245005553 ABC transporter signature motif; other site 688245005554 Walker B; other site 688245005555 D-loop; other site 688245005556 H-loop/switch region; other site 688245005557 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...; Region: TM_ABC_iron-siderophores_like; cd06550 688245005558 ABC-ATPase subunit interface; other site 688245005559 dimer interface; other site 688245005560 putative PBP binding regions; other site 688245005561 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 688245005562 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 688245005563 putative ligand binding residues; other site 688245005564 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245005565 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 688245005566 N-terminal plug; other site 688245005567 ligand-binding site; other site 688245005568 Integrase core domain; Region: rve; cl01316 688245005569 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245005570 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 688245005571 HipA-like N-terminal domain; Region: HipA_N; pfam07805 688245005572 HipA-like C-terminal domain; Region: HipA_C; pfam07804 688245005573 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005574 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005575 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 688245005576 dimerization interface; other site 688245005577 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 688245005578 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 688245005579 conserved cys residue; other site 688245005580 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245005581 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 688245005582 active site residue 688245005583 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005584 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005585 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 688245005586 putative dimerization interface; other site 688245005587 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 688245005588 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; cl01116 688245005589 Integrase core domain; Region: rve; cl01316 688245005590 Integrase core domain; Region: rve; cl01316 688245005591 putative transposase OrfB; Reviewed; Region: PHA02517 688245005592 Anti-sigma-K factor rskA; Region: RskA; cl02208 688245005593 RNA polymerase sigma factor; Provisional; Region: PRK12537 688245005594 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245005595 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...; Region: Sigma70_r4; cl01055 688245005596 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 688245005597 Predicted membrane protein [Function unknown]; Region: COG3174 688245005598 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245005599 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005600 metal-binding site 688245005601 active site 688245005602 I-site; other site 688245005603 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005604 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 688245005605 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005606 short chain dehydrogenase; Provisional; Region: PRK06101 688245005607 NAD(P) binding site; other site 688245005608 active site 688245005609 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 688245005610 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 688245005611 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 688245005612 S-adenosylmethionine binding site; other site 688245005613 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 688245005614 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 688245005615 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005616 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005617 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245005618 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 688245005619 potential frameshift: common BLAST hit: gi|226945664|ref|YP_002800737.1| Bacterial regulatory protein, GntR 688245005620 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 688245005621 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245005622 DNA binding site 688245005623 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 688245005624 pyridoxal 5'-phosphate binding site; other site 688245005625 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 688245005626 Sulfatase; Region: Sulfatase; cl10460 688245005627 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 688245005628 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245005629 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005630 NAD(P) binding site; other site 688245005631 active site 688245005632 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 688245005633 NAD(P) binding site; other site 688245005634 catalytic residues; other site 688245005635 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 688245005636 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 688245005637 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 688245005638 shikimate binding site; other site 688245005639 NAD(P) binding site; other site 688245005640 choline dehydrogenase; Validated; Region: PRK02106 688245005641 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005642 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 688245005643 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 688245005644 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 688245005645 Ligand binding site; other site 688245005646 potential frameshift: common BLAST hit: gi|160897832|ref|YP_001563414.1| electron transfer flavoprotein alpha subunit 688245005647 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 688245005648 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 688245005649 Domain of unknown function DUF; Region: DUF202; cl09954 688245005650 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 688245005651 DNA binding site 688245005652 Int/Topo IB signature motif; other site 688245005653 active site 688245005654 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 688245005655 glutathione S-transferase; Provisional; Region: PRK15113 688245005656 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245005657 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...; Region: AAA; cd00009 688245005658 Walker A motif; other site 688245005659 ATP binding site; other site 688245005660 Walker B motif; other site 688245005661 arginine finger; other site 688245005662 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 688245005663 Integrase core domain; Region: rve; cl01316 688245005664 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 688245005665 non-specific DNA binding site; other site 688245005666 salt bridge; other site 688245005667 sequence-specific DNA binding site; other site 688245005668 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 688245005669 Phage integrase family; Region: Phage_integrase; pfam00589 688245005670 DNA binding site 688245005671 Int/Topo IB signature motif; other site 688245005672 active site 688245005673 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 688245005674 Phage integrase family; Region: Phage_integrase; pfam00589 688245005675 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 include the bacteriophage lambda integrase, the...; Region: INT_REC_C; cd01182 688245005676 DNA binding site 688245005677 Int/Topo IB signature motif; other site 688245005678 active site 688245005679 catalytic residues; other site 688245005680 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 688245005681 chromosome replication initiation inhibitor protein; Provisional; Region: PRK13348 688245005682 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005683 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 688245005684 dimerization interface; other site 688245005685 LysE type translocator; Region: LysE; cl00565 688245005686 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245005687 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005689 threonine and homoserine efflux system; Provisional; Region: PRK10532 688245005690 EamA-like transporter family; Region: EamA; cl01037 688245005691 PrkA family serine protein kinase; Provisional; Region: PRK15455 688245005692 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245005693 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 688245005694 Protein of unknown function (DUF444); Region: DUF444; pfam04285 688245005695 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 688245005696 SpoVR family protein; Provisional; Region: PRK11767 688245005697 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 688245005698 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 688245005699 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3530 688245005700 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005701 metal-binding site 688245005702 active site 688245005703 I-site; other site 688245005704 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 688245005705 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245005706 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...; Region: Sigma70_r4; cl01055 688245005707 fec operon regulator FecR; Reviewed; Region: PRK09774 688245005708 FecR protein; Region: FecR; pfam04773 688245005709 Secretin and TonB N terminus short domain; Region: STN; pfam07660 688245005710 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245005711 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 688245005712 N-terminal plug; other site 688245005713 ligand-binding site; other site 688245005714 extracytoplasmic-function sigma-70 factor; Validated; Region: PRK07037 688245005715 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...; Region: Sigma70_r4; cl01055 688245005716 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 688245005717 FecR protein; Region: FecR; pfam04773 688245005718 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245005719 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 688245005720 N-terminal plug; other site 688245005721 ligand-binding site; other site 688245005722 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245005723 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 688245005724 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245005725 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 688245005726 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; cl11391 688245005727 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 688245005728 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 688245005729 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 688245005730 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 688245005731 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 688245005732 ATP binding site; other site 688245005733 putative Mg++ binding site; other site 688245005734 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 688245005735 nucleotide binding region; other site 688245005736 ATP-binding site; other site 688245005737 TRCF domain; Region: TRCF; pfam03461 688245005738 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 688245005739 substrate binding site; other site 688245005740 dimer interface; other site 688245005741 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...; Region: MECDP_synthase; cd00554 688245005742 homotrimer interaction site; other site 688245005743 zinc binding site; other site 688245005744 CDP-binding sites; other site 688245005745 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 688245005746 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245005747 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 trans-...; Region: HisKA; cl00080 688245005748 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 688245005749 ATP binding site; other site 688245005750 Mg2+ binding site; other site 688245005751 G-X-G motif; other site 688245005752 osmolarity response regulator; Provisional; Region: ompR; PRK09468 688245005753 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 688245005754 active site 688245005755 phosphorylation site 688245005756 intermolecular recognition site; other site 688245005757 dimerization interface; other site 688245005758 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...; Region: trans_reg_C; cd00383 688245005759 DNA binding site 688245005760 Protein of unknown function (DUF541); Region: SIMPL; cl01077 688245005761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005762 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 688245005763 NAD(P) binding site; other site 688245005764 active site 688245005765 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245005766 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 688245005767 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 688245005768 synthetase active site; other site 688245005769 NTP binding site; other site 688245005770 metal-binding site 688245005771 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...; Region: TGS_RelA_SpoT; cd01668 688245005772 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 688245005773 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 688245005774 Integrase core domain; Region: rve; cl01316 688245005775 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245005776 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...; Region: AAA; cd00009 688245005777 Walker A motif; other site 688245005778 ATP binding site; other site 688245005779 Walker B motif; other site 688245005780 arginine finger; other site 688245005781 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 688245005782 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 include the bacteriophage lambda integrase, the...; Region: INT_REC_C; cd01182 688245005783 DNA binding site 688245005784 Int/Topo IB signature motif; other site 688245005785 active site 688245005786 catalytic residues; other site 688245005787 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 688245005788 Anti-sigma-K factor rskA; Region: RskA; cl02208 688245005789 RNA polymerase sigma factor; Provisional; Region: PRK12514 688245005790 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245005791 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...; Region: Sigma70_r4; cd06171 688245005792 DNA binding residues 688245005793 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 688245005794 dinuclear metal binding motif; other site 688245005795 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 688245005796 Transposase; Region: Transposase_12; pfam01610 688245005797 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 688245005798 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 688245005799 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005800 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 688245005801 DNA photolyase; Region: DNA_photolyase; pfam00875 688245005802 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 688245005803 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 688245005804 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 688245005805 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 688245005806 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245005807 NAD(P) binding site; other site 688245005808 active site 688245005809 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 688245005810 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 688245005811 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 688245005812 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 688245005813 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 trans...; Region: HisKA; cd00082 688245005814 dimer interface; other site 688245005815 phosphorylation site 688245005816 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 688245005817 ATP binding site; other site 688245005818 Mg2+ binding site; other site 688245005819 G-X-G motif; other site 688245005820 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...; Region: PBPb; cd00134 688245005821 substrate binding pocket; other site 688245005822 membrane-bound complex binding site; other site 688245005823 hinge residues; other site 688245005824 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245005825 Zn2+ binding site; other site 688245005826 Mg2+ binding site; other site 688245005827 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 688245005828 active site 688245005829 phosphorylation site 688245005830 intermolecular recognition site; other site 688245005831 dimerization interface; other site 688245005832 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; cl09944 688245005833 active site 688245005834 phosphorylation site 688245005835 intermolecular recognition site; other site 688245005836 dimerization interface; other site 688245005837 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 688245005838 active site 688245005839 phosphorylation site 688245005840 intermolecular recognition site; other site 688245005841 dimerization interface; other site 688245005842 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; cl00086 688245005843 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 688245005844 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245005845 dimerization interface; other site 688245005846 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245005847 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245005848 potential frameshift: common BLAST hit: gi|160897199|ref|YP_001562781.1| integrase catalytic region 688245005849 Integrase core domain; Region: rve; cl01316 688245005850 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 688245005851 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 688245005852 heme-binding site; other site 688245005853 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 688245005854 PAS fold; Region: PAS_3; pfam08447 688245005855 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245005856 metal-binding site 688245005857 active site 688245005858 I-site; other site 688245005859 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 688245005860 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 688245005861 PAS fold; Region: PAS_3; pfam08447 688245005862 putative active site; other site 688245005863 heme pocket; other site 688245005864 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245005865 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245005866 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245005867 Phage integrase family; Region: Phage_integrase; pfam00589 688245005868 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 include the bacteriophage lambda integrase, the...; Region: INT_REC_C; cd01182 688245005869 DNA binding site 688245005870 Int/Topo IB signature motif; other site 688245005871 active site 688245005872 catalytic residues; other site 688245005873 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 688245005874 Cytochrome C biogenesis protein; Region: CcmH; cl01179 688245005875 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 688245005876 catalytic residues; other site 688245005877 central insert; other site 688245005878 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 688245005879 CcmE; Region: CcmE; cl00994 688245005880 Heme exporter protein D (CcmD); Region: CcmD; cl11475 688245005881 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 688245005882 CcmB protein; Region: CcmB; cl01016 688245005883 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245005884 Walker A/P-loop; other site 688245005885 ATP binding site; other site 688245005886 Q-loop/lid; other site 688245005887 ABC transporter signature motif; other site 688245005888 Walker B; other site 688245005889 D-loop; other site 688245005890 H-loop/switch region; other site 688245005891 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 688245005892 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 688245005893 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 688245005894 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 688245005895 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 oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 688245005896 [4Fe-4S] binding site; other site 688245005897 molybdopterin cofactor binding site; other site 688245005898 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 oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 688245005899 molybdopterin cofactor binding site; other site 688245005900 NapD protein; Region: NapD; cl01163 688245005901 Periplasmic nitrate reductase protein NapE; Region: NapE; cl01848 688245005902 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245005903 classical (c) SDRs; Region: SDR_c; cd05233 688245005904 NAD(P) binding site; other site 688245005905 active site 688245005906 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_4; cd07822 688245005907 putative hydrophobic ligand binding site; other site 688245005908 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 688245005909 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 688245005910 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 688245005911 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 688245005912 CysD dimerization site; other site 688245005913 G1 box; other site 688245005914 putative GEF interaction site; other site 688245005915 GTP/Mg2+ binding site; other site 688245005916 Switch I region; other site 688245005917 G2 box; other site 688245005918 G3 box; other site 688245005919 Switch II region; other site 688245005920 G4 box; other site 688245005921 G5 box; other site 688245005922 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...; Region: CysN_NodQ_II; cd03695 688245005923 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...; Region: CysN_NoDQ_III; cd04095 688245005924 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation...; Region: APSK; cd02027 688245005925 ligand-binding site; other site 688245005926 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 688245005927 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 688245005928 Active Sites; active site 688245005929 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 688245005930 active site 688245005931 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 688245005932 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005933 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005934 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 688245005935 putative effector binding pocket; other site 688245005936 putative dimerization interface; other site 688245005937 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245005938 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...; Region: FNR_like; cl06868 688245005939 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245005940 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 688245005941 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245005942 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245005943 DNA polymerase type-B family; Region: POLBc; smart00486 688245005944 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245005945 DNA polymerase family B; Region: DNA_pol_B; pfam00136 688245005946 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 688245005947 active site 688245005948 metal-binding site 688245005949 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005950 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005951 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 688245005952 dimerization interface; other site 688245005953 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 688245005954 hypothetical protein; Provisional; Region: PRK06126 688245005955 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245005956 allantoate amidohydrolase; Reviewed; Region: PRK12890 688245005957 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245005958 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245005959 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245005960 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245005961 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 688245005962 putative dimerization interface; other site 688245005963 YeeE/YedE family (DUF395); Region: DUF395; cl01018 688245005964 YeeE/YedE family (DUF395); Region: DUF395; cl01018 688245005965 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 688245005966 dimerization interface; other site 688245005967 putative DNA binding site; other site 688245005968 putative Zn2+ binding site; other site 688245005969 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245005970 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245005971 Uncharacterized conserved protein [Function unknown]; Region: COG5361 688245005972 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 688245005973 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 688245005974 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 688245005975 Uncharacterized conserved protein [Function unknown]; Region: COG5361 688245005976 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 688245005977 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 688245005978 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 688245005979 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein; Region: ABC_MetN_methionine_transporter; cd03258 688245005980 Walker A/P-loop; other site 688245005981 ATP binding site; other site 688245005982 Q-loop/lid; other site 688245005983 ABC transporter signature motif; other site 688245005984 Walker B; other site 688245005985 D-loop; other site 688245005986 H-loop/switch region; other site 688245005987 NIL domain; Region: NIL; pfam09383 688245005988 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...; Region: TM_PBP2; cd06261 688245005989 dimer interface; other site 688245005990 conserved gate region; other site 688245005991 ABC-ATPase subunit interface; other site 688245005992 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 688245005993 generic binding surface I; other site 688245005994 generic binding surface II; other site 688245005995 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 688245005996 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a...; Region: Nitroreductase; cd02136 688245005997 putative FMN binding site; other site 688245005998 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 688245005999 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 688245006000 dimer interface; other site 688245006001 active site 688245006002 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006003 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 688245006004 BioY family; Region: BioY; cl00560 688245006005 Cobalt transport protein; Region: CbiQ; cl00463 688245006006 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 688245006007 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 688245006008 Walker A/P-loop; other site 688245006009 ATP binding site; other site 688245006010 Q-loop/lid; other site 688245006011 ABC transporter signature motif; other site 688245006012 Walker B; other site 688245006013 D-loop; other site 688245006014 H-loop/switch region; other site 688245006015 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245006016 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 688245006017 N-terminal plug; other site 688245006018 ligand-binding site; other site 688245006019 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006020 Acyl-CoA reductase LuxC; Region: ALDH_Acyl-CoA-Red_LuxC; cd07080 688245006021 Acyl-CoA reductase (LuxC); Region: LuxC; pfam05893 688245006022 putative catalytic cysteine; other site 688245006023 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245006024 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245006025 Walker A/P-loop; other site 688245006026 ATP binding site; other site 688245006027 Q-loop/lid; other site 688245006028 ABC transporter signature motif; other site 688245006029 Walker B; other site 688245006030 D-loop; other site 688245006031 H-loop/switch region; other site 688245006032 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...; Region: TM_PBP2; cl00427 688245006033 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 688245006034 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 688245006035 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245006036 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245006037 NAD(P) binding site; other site 688245006038 active site 688245006039 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245006040 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245006041 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006042 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 688245006043 putative effector binding pocket; other site 688245006044 putative dimerization interface; other site 688245006045 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; cl12031 688245006046 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 688245006047 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...; Region: TM_PBP2; cd06261 688245006048 dimer interface; other site 688245006049 conserved gate region; other site 688245006050 putative PBP binding loops; other site 688245006051 ABC-ATPase subunit interface; other site 688245006052 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...; Region: TM_PBP2; cd06261 688245006053 dimer interface; other site 688245006054 conserved gate region; other site 688245006055 putative PBP binding loops; other site 688245006056 ABC-ATPase subunit interface; other site 688245006057 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 688245006058 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-...; Region: ABC_CysA_sulfate_importer; cd03296 688245006059 Walker A/P-loop; other site 688245006060 ATP binding site; other site 688245006061 Q-loop/lid; other site 688245006062 ABC transporter signature motif; other site 688245006063 Walker B; other site 688245006064 D-loop; other site 688245006065 H-loop/switch region; other site 688245006066 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 688245006067 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 688245006068 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245006069 Glutathione S-transferase (GST) family, C-terminal alpha helical 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...; Region: GST_C_family; cl02776 688245006070 N-terminal domain interface; other site 688245006071 dimer interface; other site 688245006072 substrate binding pocket (H-site); other site 688245006073 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245006074 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006075 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 688245006076 dimerization interface; other site 688245006077 Beta-lactamase; Region: Beta-lactamase; cl01009 688245006078 RNA polymerase sigma factor; Reviewed; Region: PRK12527 688245006079 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...; Region: Sigma70_r4; cl01055 688245006080 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 688245006081 FecR protein; Region: FecR; pfam04773 688245006082 Secretin and TonB N terminus short domain; Region: STN; pfam07660 688245006083 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245006084 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 688245006085 N-terminal plug; other site 688245006086 ligand-binding site; other site 688245006087 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245006088 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 688245006089 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 688245006090 putative ion selectivity filter; other site 688245006091 putative pore gating glutamate residue; other site 688245006092 putative H+/Cl- coupling transport residue; other site 688245006093 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 5,10-...; Region: DHFR; cl00161 688245006094 ribonucleotide reductase-like protein; Provisional; Region: PRK06948 688245006095 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 688245006096 dimer interface; other site 688245006097 active site 688245006098 effector binding site; other site 688245006099 2-isopropylmalate synthase; Validated; Region: PRK03739 688245006100 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 688245006101 active site 688245006102 catalytic residues; other site 688245006103 metal-binding site 688245006104 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 688245006105 Cupin domain; Region: Cupin_2; cl09118 688245006106 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245006107 N-acetylglutamate synthase; Validated; Region: PRK05279 688245006108 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 N-...; Region: AAK_NAGS-ABP; cd04237 688245006109 putative feedback inhibition sensing region; other site 688245006110 putative nucleotide binding site; other site 688245006111 putative substrate binding site; other site 688245006112 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245006113 Coenzyme A binding pocket; other site 688245006114 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245006115 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245006116 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 688245006117 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...; Region: VirB11-like_ATPase; cd01130 688245006118 ATP binding site; other site 688245006119 Walker A motif; other site 688245006120 hexamer interface; other site 688245006121 Walker B motif; other site 688245006122 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 688245006123 active site 688245006124 phosphorylation site 688245006125 intermolecular recognition site; other site 688245006126 dimerization interface; other site 688245006127 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 688245006128 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly...; Region: CpaE_like; cd03111 688245006129 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly...; Region: CpaE_like; cd03111 688245006130 TadE-like protein; Region: TadE; pfam07811 688245006131 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 688245006132 TadE-like protein; Region: TadE; pfam07811 688245006133 Flp/Fap pilin component; Region: Flp_Fap; cl01585 688245006134 Flp/Fap pilin component; Region: Flp_Fap; cl01585 688245006135 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 688245006136 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 688245006137 SAF domain; Region: SAF; cl00555 688245006138 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 688245006139 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 688245006140 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245006141 putative substrate translocation pore; other site 688245006142 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245006143 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 688245006144 N-terminal plug; other site 688245006145 ligand-binding site; other site 688245006146 enterobactin/ferric enterobactin esterase; Provisional; Region: PRK10439 688245006147 Domain of unknown function (DUF3327); Region: DUF3327; pfam11806 688245006148 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; cl12031 688245006149 Predicted membrane protein [Function unknown]; Region: COG5373 688245006150 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245006151 active site 688245006152 metal-binding site 688245006153 DEAD-like helicases superfamily; Region: DEXDc; smart00487 688245006154 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 688245006155 ATP binding site; other site 688245006156 putative Mg++ binding site; other site 688245006157 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 688245006158 nucleotide binding region; other site 688245006159 ATP-binding site; other site 688245006160 Helicase associated domain (HA2); Region: HA2; cl04503 688245006161 Domain of unknown function (DUF1605); Region: DUF1605; pfam07717 688245006162 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 688245006163 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006164 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006165 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 688245006166 putative effector binding pocket; other site 688245006167 putative dimerization interface; other site 688245006168 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 688245006169 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245006170 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 688245006171 NodT family; Region: outer_NodT; TIGR01845 688245006172 Outer membrane efflux protein; Region: OEP; pfam02321 688245006173 Outer membrane efflux protein; Region: OEP; pfam02321 688245006174 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 688245006175 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245006176 Beta-Casp domain; Region: Beta-Casp; pfam10996 688245006177 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 688245006178 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08314 688245006179 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006180 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 688245006181 SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of...; Region: SelB; cd04171 688245006182 G1 box; other site 688245006183 putative GEF interaction site; other site 688245006184 GTP/Mg2+ binding site; other site 688245006185 Switch I region; other site 688245006186 G2 box; other site 688245006187 G3 box; other site 688245006188 Switch II region; other site 688245006189 G4 box; other site 688245006190 G5 box; other site 688245006191 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires...; Region: selB_II; cd03696 688245006192 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 688245006193 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 688245006194 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 688245006195 selenocysteine synthase; Provisional; Region: PRK04311 688245006196 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 688245006197 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 688245006198 pyridoxal 5'-phosphate binding pocket; other site 688245006199 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 688245006200 catalytic residue; other site 688245006201 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564; cl11689 688245006202 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 688245006203 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 688245006204 Fe-S containing; Region: FDH-beta; TIGR01582 688245006205 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 688245006206 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 688245006207 molybdopterin cofactor binding site; other site 688245006208 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 688245006209 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 688245006210 molybdopterin cofactor binding site; other site 688245006211 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 688245006212 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 688245006213 Domain of unknown function DUF20; Region: UPF0118; cl00465 688245006214 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 688245006215 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 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 688245006216 TPP-binding site; other site 688245006217 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 688245006218 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 688245006219 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 688245006220 E3 interaction surface; other site 688245006221 lipoyl attachment site; other site 688245006222 e3 binding domain; Region: E3_binding; pfam02817 688245006223 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 688245006224 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 688245006225 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006226 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 688245006227 Predicted ATPase [General function prediction only]; Region: COG1485 688245006228 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 688245006229 active site 688245006230 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 688245006231 CRISPR/Cas system-associated DinG family helicase Csf4; Region: csf4_Type-U; cl09250 688245006232 CRISPR/Cas system-associated DinG family helicase Csf4; Region: csf4_Type-U; cl09250 688245006233 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 688245006234 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 688245006235 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 688245006236 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 688245006237 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...; Region: DnaE_OBF; cd04485 688245006238 generic binding surface II; other site 688245006239 generic binding surface I; other site 688245006240 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 688245006241 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 688245006242 Clp amino terminal domain; Region: Clp_N; pfam02861 688245006243 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...; Region: AAA; cd00009 688245006244 Walker A motif; other site 688245006245 ATP binding site; other site 688245006246 Walker B motif; other site 688245006247 arginine finger; other site 688245006248 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...; Region: AAA; cd00009 688245006249 Walker A motif; other site 688245006250 ATP binding site; other site 688245006251 Walker B motif; other site 688245006252 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 688245006253 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 688245006254 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 688245006255 active site 688245006256 phosphorylation site 688245006257 intermolecular recognition site; other site 688245006258 dimerization interface; other site 688245006259 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245006260 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 688245006261 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 688245006262 ATP binding site; other site 688245006263 Mg2+ binding site; other site 688245006264 G-X-G motif; other site 688245006265 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 688245006266 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 688245006267 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 688245006268 Subunit I/III interface; other site 688245006269 Subunit III/IV interface; other site 688245006270 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 688245006271 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 688245006272 D-pathway; other site 688245006273 Putative ubiquinol binding site; other site 688245006274 Low-spin heme (heme b) binding site; other site 688245006275 Putative water exit pathway; other site 688245006276 Binuclear center (heme o3/CuB); other site 688245006277 K-pathway; other site 688245006278 Putative proton exit pathway; other site 688245006279 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 688245006280 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 688245006281 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 688245006282 metabolite-proton symporter; Region: 2A0106; TIGR00883 688245006283 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 688245006284 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 688245006285 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006286 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006287 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 688245006288 putative dimerization interface; other site 688245006289 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 688245006290 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006291 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245006292 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 688245006293 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006294 Uncharacterized protein conserved in bacteria (DUF2257); Region: DUF2257; cl01794 688245006295 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 688245006296 Ligand Binding Site; other site 688245006297 hypothetical protein; Provisional; Region: PRK00808 688245006298 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 688245006299 octamerization interface; other site 688245006300 diferric-oxygen binding site; other site 688245006301 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 688245006302 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245006303 NAD(P) binding site; other site 688245006304 active site 688245006305 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245006306 Q-loop/lid; other site 688245006307 ABC transporter signature motif; other site 688245006308 Walker B; other site 688245006309 D-loop; other site 688245006310 H-loop/switch region; other site 688245006311 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 688245006312 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245006313 Walker A/P-loop; other site 688245006314 ATP binding site; other site 688245006315 Q-loop/lid; other site 688245006316 ABC transporter signature motif; other site 688245006317 Walker B; other site 688245006318 D-loop; other site 688245006319 H-loop/switch region; other site 688245006320 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 688245006321 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 688245006322 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 688245006323 TM-ABC transporter signature motif; other site 688245006324 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 688245006325 TM-ABC transporter signature motif; other site 688245006326 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245006327 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 688245006328 dimerization interface; other site 688245006329 ligand binding site; other site 688245006330 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 688245006331 active site 688245006332 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 688245006333 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 688245006334 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 trans...; Region: HisKA; cd00082 688245006335 dimer interface; other site 688245006336 phosphorylation site 688245006337 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 688245006338 ATP binding site; other site 688245006339 Mg2+ binding site; other site 688245006340 G-X-G motif; other site 688245006341 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 688245006342 active site 688245006343 phosphorylation site 688245006344 intermolecular recognition site; other site 688245006345 dimerization interface; other site 688245006346 glycine dehydrogenase; Provisional; Region: PRK05367 688245006347 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 688245006348 pyridoxal 5'-phosphate binding pocket; other site 688245006349 catalytic residue; other site 688245006350 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...; Region: GDC-P; cd00613 688245006351 tetramer interface; other site 688245006352 pyridoxal 5'-phosphate binding site; other site 688245006353 catalytic residue; other site 688245006354 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4884 688245006355 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 L...; Region: GCS_H; cd06848 688245006356 lipoyl attachment site; other site 688245006357 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 688245006358 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 688245006359 Gram-negative bacterial tonB protein; Region: TonB; cl10048 688245006360 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245006361 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 688245006362 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 688245006363 putative substrate translocation pore; other site 688245006364 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 688245006365 NodT family; Region: outer_NodT; TIGR01845 688245006366 Outer membrane efflux protein; Region: OEP; pfam02321 688245006367 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245006368 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006369 Copper resistance protein D; Region: CopD; cl00563 688245006370 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 688245006371 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 688245006372 dimer interface; other site 688245006373 active site 688245006374 heme binding site; other site 688245006375 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 688245006376 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 688245006377 PAS domain S-box; Region: sensory_box; TIGR00229 688245006378 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...; Region: LuxR_C_like; cd06170 688245006379 DNA binding residues 688245006380 dimerization interface; other site 688245006381 Coenzyme A transferase; Region: CoA_trans; cl00773 688245006382 Coenzyme A transferase; Region: CoA_trans; cl00773 688245006383 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245006384 Zn2+ binding site; other site 688245006385 Mg2+ binding site; other site 688245006386 Cell division inhibitor SulA; Region: SulA; cl01880 688245006387 DNA Polymerase Y-family; Region: PolY_like; cd03468 688245006388 DNA binding site 688245006389 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 688245006390 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 688245006391 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 688245006392 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 688245006393 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...; Region: DnaE_OBF; cd04485 688245006394 generic binding surface II; other site 688245006395 generic binding surface I; other site 688245006396 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245006397 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006398 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 688245006399 dimerization interface; other site 688245006400 substrate binding pocket; other site 688245006401 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 688245006402 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245006403 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245006404 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 688245006405 active site 2 688245006406 active site 1 688245006407 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 688245006408 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245006409 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245006410 active site 688245006411 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245006412 enoyl-CoA hydratase; Provisional; Region: PRK09245 688245006413 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 688245006414 substrate binding site; other site 688245006415 oxyanion hole (OAH) forming residues; other site 688245006416 trimer interface; other site 688245006417 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 688245006418 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245006419 dimerization interface; other site 688245006420 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245006421 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245006422 agmatine deiminase; Region: agmatine_aguA; TIGR03380 688245006423 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 688245006424 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 688245006425 agmatine deiminase; Region: agmatine_aguA; TIGR03380 688245006426 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245006427 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006428 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 688245006429 dimerization interface; other site 688245006430 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 688245006431 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006432 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006433 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 688245006434 dimerization interface; other site 688245006435 Arylsulfotransferase (ASST); Region: Arylsulfotrans; pfam05935 688245006436 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 688245006437 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 688245006438 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSRA_1; cd02558 688245006439 probable active site; other site 688245006440 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245006441 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245006442 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 688245006443 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 688245006444 putative substrate translocation pore; other site 688245006445 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 688245006446 NodT family; Region: outer_NodT; TIGR01845 688245006447 Outer membrane efflux protein; Region: OEP; pfam02321 688245006448 Outer membrane efflux protein; Region: OEP; pfam02321 688245006449 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; cl00364 688245006450 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; cl00364 688245006451 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 688245006452 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 688245006453 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 688245006454 catalytic triad; other site 688245006455 K+ potassium transporter; Region: K_trans; cl01227 688245006456 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245006457 VRR-NUC domain; Region: VRR_NUC; pfam08774 688245006458 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 688245006459 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; cl12029 688245006460 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 688245006461 CRISPR/Cas system-associated DinG family helicase Csf4; Region: csf4_Type-U; cl09250 688245006462 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 688245006463 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 688245006464 homodimer interaction site; other site 688245006465 cofactor binding site; other site 688245006466 TOBE domain; Region: TOBE_2; cl01440 688245006467 TOBE domain; Region: TOBE_2; cl01440 688245006468 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245006469 Coenzyme A binding pocket; other site 688245006470 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245006471 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 688245006472 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 688245006473 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245006474 Walker A/P-loop; other site 688245006475 ATP binding site; other site 688245006476 ABC transporter signature motif; other site 688245006477 Walker B; other site 688245006478 D-loop; other site 688245006479 H-loop/switch region; other site 688245006480 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 688245006481 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245006482 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006483 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 688245006484 dimerization interface; other site 688245006485 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 688245006486 active site 688245006487 metal-binding site 688245006488 Protein of unknown function DUF2625; Region: DUF2625; cl08177 688245006489 Protein of unknown function (DUF1697); Region: DUF1697; cl01557 688245006490 tetrathionate reductase subunit A; Provisional; Region: PRK14991 688245006491 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 688245006492 molybdopterin cofactor binding site; other site 688245006493 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 688245006494 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 688245006495 putative molybdopterin cofactor binding site; other site 688245006496 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl01295 688245006497 tetrathionate reductase subunit B; Provisional; Region: PRK14993 688245006498 4Fe-4S binding domain; Region: Fer4; pfam00037 688245006499 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 688245006500 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...; Region: DHOD_2_like; cd04738 688245006501 quinone interaction residues; other site 688245006502 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 688245006503 active site 688245006504 catalytic residues; other site 688245006505 FMN binding site; other site 688245006506 substrate binding site; other site 688245006507 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 688245006508 tetramer (dimer of dimers) interface; other site 688245006509 active site 688245006510 dimer interface; other site 688245006511 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...; Region: NrdH; cd02976 688245006512 catalytic residues; other site 688245006513 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 688245006514 Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and...; Region: M3A_DCP_Oligopeptidase_A; cd06456 688245006515 active site 688245006516 zinc binding site; other site 688245006517 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 688245006518 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 688245006519 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 688245006520 homodimer interface; other site 688245006521 NADP binding site; other site 688245006522 substrate binding site; other site 688245006523 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 688245006524 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 688245006525 active site 688245006526 phosphorylation site 688245006527 intermolecular recognition site; other site 688245006528 dimerization interface; other site 688245006529 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...; Region: LuxR_C_like; cd06170 688245006530 DNA binding residues 688245006531 dimerization interface; other site 688245006532 PAS domain S-box; Region: sensory_box; TIGR00229 688245006533 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 688245006534 putative active site; other site 688245006535 heme pocket; other site 688245006536 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 trans-...; Region: HisKA; cl00080 688245006537 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 688245006538 ATP binding site; other site 688245006539 Mg2+ binding site; other site 688245006540 G-X-G motif; other site 688245006541 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 688245006542 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 688245006543 dimer interface; other site 688245006544 TPP-binding site; other site 688245006545 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 688245006546 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 688245006547 E3 interaction surface; other site 688245006548 lipoyl attachment site; other site 688245006549 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 688245006550 E3 interaction surface; other site 688245006551 lipoyl attachment site; other site 688245006552 e3 binding domain; Region: E3_binding; pfam02817 688245006553 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 688245006554 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 688245006555 E3 interaction surface; other site 688245006556 lipoyl attachment site; other site 688245006557 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006558 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 688245006559 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 688245006560 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 688245006561 non-specific DNA binding site; other site 688245006562 salt bridge; other site 688245006563 sequence-specific DNA binding site; other site 688245006564 HipA N-terminal domain; Region: couple_hipA; TIGR03071 688245006565 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 688245006566 HipA-like N-terminal domain; Region: HipA_N; pfam07805 688245006567 HipA-like C-terminal domain; Region: HipA_C; pfam07804 688245006568 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 688245006569 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 688245006570 d-galactonate transporter; Region: 2A0114; TIGR00893 688245006571 putative substrate translocation pore; other site 688245006572 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 688245006573 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 688245006574 PhnA protein; Region: PhnA; pfam03831 688245006575 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 688245006576 MoxR-like ATPases [General function prediction only]; Region: COG0714 688245006577 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...; Region: AAA; cd00009 688245006578 Walker A motif; other site 688245006579 ATP binding site; other site 688245006580 Walker B motif; other site 688245006581 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006582 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006583 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 688245006584 dimerization interface; other site 688245006585 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 688245006586 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245006587 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245006588 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 688245006589 uncharacterized enzyme; Region: gshA_cyan_rel; TIGR02050 688245006590 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245006591 metal-binding site 688245006592 active site 688245006593 I-site; other site 688245006594 Protein of unknown function (DUF2167); Region: DUF2167; cl01938 688245006595 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...; Region: Aldo_ket_red; cd06660 688245006596 active site 688245006597 catalytic tetrad; other site 688245006598 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 688245006599 putative substrate translocation pore; other site 688245006600 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 688245006601 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 688245006602 active site 688245006603 Predicted membrane protein [Function unknown]; Region: COG4129 688245006604 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245006605 ethanolamine permease; Region: 2A0305; TIGR00908 688245006606 Protein of unknown function DUF55; Region: DUF55; cl00728 688245006607 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 688245006608 NlpC/P60 family; Region: NLPC_P60; cl11438 688245006609 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 688245006610 Isochorismatase family; Region: Isochorismatase; pfam00857 688245006611 catalytic triad; other site 688245006612 dimer interface; other site 688245006613 conserved cis-peptide bond; other site 688245006614 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 688245006615 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 688245006616 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006617 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 688245006618 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 688245006619 active site 688245006620 substrate binding site; other site 688245006621 metal-binding site 688245006622 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 688245006623 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 688245006624 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 688245006625 Outer membrane efflux protein; Region: OEP; pfam02321 688245006626 Outer membrane efflux protein; Region: OEP; pfam02321 688245006627 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 688245006628 active site residue 688245006629 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 688245006630 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 688245006631 S-adenosylmethionine binding site; other site 688245006632 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 688245006633 Protein export membrane protein; Region: SecD_SecF; cl14618 688245006634 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245006635 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 688245006636 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 688245006637 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 688245006638 N-terminal plug; other site 688245006639 ligand-binding site; other site 688245006640 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 688245006641 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 include the bacteriophage lambda integrase, the...; Region: INT_REC_C; cd01182 688245006642 DNA binding site 688245006643 Int/Topo IB signature motif; other site 688245006644 active site 688245006645 catalytic residues; other site 688245006646 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 688245006647 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 688245006648 Pyridoxine 5'-phosphate oxidase C-terminal dimerization region; Region: PNPOx_C; pfam10590 688245006649 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 688245006650 Ligand binding site; other site 688245006651 metal-binding site 688245006652 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 688245006653 E-class dimer interface; other site 688245006654 P-class dimer interface; other site 688245006655 active site 688245006656 Cu2+ binding site; other site 688245006657 Zn2+ binding site; other site 688245006658 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 688245006659 putative active site pocket; other site 688245006660 dimerization interface; other site 688245006661 putative catalytic residue; other site 688245006662 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245006663 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245006664 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006665 putative acyl-CoA synthetase; Provisional; Region: PRK06018 688245006666 enoyl-CoA hydratase; Provisional; Region: PRK08150 688245006667 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 688245006668 substrate binding site; other site 688245006669 oxyanion hole (OAH) forming residues; other site 688245006670 trimer interface; other site 688245006671 Protein of unknown function, DUF485; Region: DUF485; cl01231 688245006672 Sodium:solute symporter family; Region: SSF; cl00456 688245006673 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 688245006674 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 688245006675 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245006676 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 688245006677 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 688245006678 tetrameric interface; other site 688245006679 NAD binding site; other site 688245006680 catalytic residues; other site 688245006681 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 688245006682 dimer interface; other site 688245006683 active site 688245006684 glutathione binding site; other site 688245006685 metal-binding site 688245006686 putative replication initiation protein; Region: PHA00330 688245006687 Zonular occludens toxin (Zot); Region: Zot; cl01706 688245006688 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 688245006689 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 688245006690 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006691 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006692 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 688245006693 putative dimerization interface; other site 688245006694 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 688245006695 pyridoxal 5'-phosphate binding site; other site 688245006696 homodimer interface; other site 688245006697 catalytic residue; other site 688245006698 aspartate-alanine antiporter; Region: Asp_Ala_antiprt; TIGR03802 688245006699 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 688245006700 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; cl09110 688245006701 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; cl09110 688245006702 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 688245006703 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 688245006704 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 688245006705 Phage integrase family; Region: Phage_integrase; pfam00589 688245006706 DNA binding site 688245006707 Int/Topo IB signature motif; other site 688245006708 active site 688245006709 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 688245006710 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; cl12031 688245006711 substrate binding pocket; other site 688245006712 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 688245006713 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 688245006714 dimer interface; other site 688245006715 substrate binding site; other site 688245006716 metal-binding site 688245006717 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 688245006718 putative active site; other site 688245006719 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 688245006720 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245006721 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245006722 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245006723 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 688245006724 carboxyltransferase (CT) interaction site; other site 688245006725 biotinylation site; other site 688245006726 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 688245006727 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245006728 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245006729 membrane ATPase/protein kinase; Provisional; Region: PRK09435 688245006730 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 688245006731 Walker A; other site 688245006732 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 688245006733 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...; Region: MM_CoA_mutase_alpha_like; cd03679 688245006734 active site 688245006735 substrate binding site; other site 688245006736 coenzyme B12 binding site; other site 688245006737 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...; Region: MM_CoA_mut_B12_BD; cd02071 688245006738 B12 binding site; other site 688245006739 cobalt ligand; other site 688245006740 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245006741 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245006742 DNA binding site 688245006743 FCD domain; Region: FCD; cl11656 688245006744 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 688245006745 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 688245006746 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 688245006747 PAS domain S-box; Region: sensory_box; TIGR00229 688245006748 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 688245006749 putative active site; other site 688245006750 heme pocket; other site 688245006751 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 688245006752 PAS fold; Region: PAS_4; pfam08448 688245006753 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 688245006754 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006755 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245006756 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 688245006757 Cache domain; Region: Cache_1; pfam02743 688245006758 IS2 transposase TnpB; Reviewed; Region: PRK09409 688245006759 Integrase core domain; Region: rve; cl01316 688245006760 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; cl01116 688245006761 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245006762 metal-binding site 688245006763 active site 688245006764 I-site; other site 688245006765 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 688245006766 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...; Region: DUS_like_FMN; cd02801 688245006767 FMN binding site; other site 688245006768 active site 688245006769 catalytic residues; other site 688245006770 substrate binding site; other site 688245006771 potential frameshift: common BLAST hit: gi|160899057|ref|YP_001564639.1| polyhydroxyalkanoate depolymerase, intracellular 688245006772 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 688245006773 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; cl12031 688245006774 ferredoxin; Provisional; Region: PRK06991 688245006775 Putative Fe-S cluster; Region: FeS; pfam04060 688245006776 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245006777 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245006778 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 688245006779 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 688245006780 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 688245006781 pyridoxal 5'-phosphate binding site; other site 688245006782 homodimer interface; other site 688245006783 catalytic residue; other site 688245006784 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 688245006785 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 688245006786 active site 688245006787 substrate binding site; other site 688245006788 trimer interface; other site 688245006789 CoA binding site; other site 688245006790 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 688245006791 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245006792 Walker A motif; other site 688245006793 ATP binding site; other site 688245006794 Walker B motif; other site 688245006795 succinyl-diaminopimelate desuccinylase, proteobacterial clade; Region: dapE_proteo; TIGR01246 688245006796 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245006797 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 688245006798 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 688245006799 S-adenosylmethionine binding site; other site 688245006800 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 688245006801 dinuclear metal binding motif; other site 688245006802 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 688245006803 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245006804 Walker A/P-loop; other site 688245006805 ATP binding site; other site 688245006806 Q-loop/lid; other site 688245006807 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245006808 ABC transporter signature motif; other site 688245006809 Walker B; other site 688245006810 D-loop; other site 688245006811 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 688245006812 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 688245006813 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 688245006814 NAD(P) binding site; other site 688245006815 homotetramer interface; other site 688245006816 homodimer interface; other site 688245006817 active site 688245006818 putative acyltransferase; Provisional; Region: PRK05790 688245006819 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 688245006820 dimer interface; other site 688245006821 active site 688245006822 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 688245006823 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 688245006824 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; cl12031 688245006825 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 688245006826 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 688245006827 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 688245006828 maleylacetoacetate isomerase; Region: maiA; TIGR01262 688245006829 C-terminal domain interface; other site 688245006830 GSH binding site (G-site); other site 688245006831 putative dimer interface; other site 688245006832 GST_C 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_C_Zeta; cd03191 688245006833 dimer interface; other site 688245006834 N-terminal domain interface; other site 688245006835 putative maleylacetoacetate (MAA) substrate binding site (H site); other site 688245006836 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245006837 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 688245006838 nudix motif; other site 688245006839 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 688245006840 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 688245006841 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245006842 metal-binding site 688245006843 active site 688245006844 I-site; other site 688245006845 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 688245006846 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 688245006847 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 688245006848 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 688245006849 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006850 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006851 Uncharacterized conserved protein [Function unknown]; Region: COG1739 688245006852 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 688245006853 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 688245006854 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; cl12031 688245006855 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245006856 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006857 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 688245006858 dimerization interface; other site 688245006859 LysE type translocator; Region: LysE; cl00565 688245006860 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 688245006861 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245006862 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245006863 YceI-like domain; Region: YceI; cl01001 688245006864 YceI-like domain; Region: YceI; cl01001 688245006865 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_11; cd08866 688245006866 putative hydrophobic ligand binding site; other site 688245006867 hypothetical protein; Reviewed; Region: PRK09588 688245006868 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 688245006869 Protein of unknown function, DUF393; Region: DUF393; cl01136 688245006870 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245006871 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 688245006872 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 688245006873 active site 688245006874 phosphorylation site 688245006875 intermolecular recognition site; other site 688245006876 dimerization interface; other site 688245006877 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...; Region: AAA; cd00009 688245006878 Walker A motif; other site 688245006879 ATP binding site; other site 688245006880 Walker B motif; other site 688245006881 arginine finger; other site 688245006882 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245006883 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 688245006884 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 trans-...; Region: HisKA; cl00080 688245006885 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 688245006886 ATP binding site; other site 688245006887 Mg2+ binding site; other site 688245006888 G-X-G motif; other site 688245006889 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 688245006890 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...; Region: 4HBT; cd00586 688245006891 active site 688245006892 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 688245006893 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006894 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 688245006895 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 688245006896 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 688245006897 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 688245006898 zinc binding site; other site 688245006899 putative ligand binding site; other site 688245006900 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 688245006901 TM-ABC transporter signature motif; other site 688245006902 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 688245006903 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245006904 Walker A/P-loop; other site 688245006905 ATP binding site; other site 688245006906 Q-loop/lid; other site 688245006907 ABC transporter signature motif; other site 688245006908 Walker B; other site 688245006909 D-loop; other site 688245006910 H-loop/switch region; other site 688245006911 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245006912 Amino acid permease; Region: AA_permease; pfam00324 688245006913 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 688245006914 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 688245006915 Permease family; Region: Xan_ur_permease; cl00967 688245006916 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 688245006917 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245006918 metal-binding site 688245006919 active site 688245006920 I-site; other site 688245006921 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 688245006922 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...; Region: MinD; cd02036 688245006923 P-loop; other site 688245006924 ADP binding residues; other site 688245006925 Switch I; other site 688245006926 Switch II; other site 688245006927 rhodanese superfamily protein; Provisional; Region: PRK05320 688245006928 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 688245006929 active site residue 688245006930 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245006931 DoxX; Region: DoxX; cl00976 688245006932 Cupin domain; Region: Cupin_2; cl09118 688245006933 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245006934 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006935 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 688245006936 dimerization interface; other site 688245006937 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006938 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245006939 HIGH motif; other site 688245006940 active site 688245006941 nucleotide binding site; other site 688245006942 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245006943 KMSKS motif; other site 688245006944 active site 688245006945 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; cl12011 688245006946 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 688245006947 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 formation...; Region: AlaRS_core; cd00673 688245006948 active site 688245006949 motif 2; other site 688245006950 motif 3; other site 688245006951 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 688245006952 SmpB protein; Region: SmpB; cl00482 688245006953 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 688245006954 putative coenzyme Q binding site; other site 688245006955 Uncharacterized protein family (UPF0125); Region: UPF0125; cl01096 688245006956 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 688245006957 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; cl09108 688245006958 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 key...; Region: CBS_pair_IMPDH; cd04601 688245006959 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 the...; Region: IMPDH; cd00381 688245006960 active site 688245006961 Phd_YefM; Region: PhdYeFM; cl09153 688245006962 PIN domain; Region: PIN; cl09128 688245006963 GMP synthase; Reviewed; Region: guaA; PRK00074 688245006964 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 688245006965 AMP/PPi binding site; other site 688245006966 candidate oxyanion hole; other site 688245006967 catalytic triad; other site 688245006968 potential glutamine specificity residues; other site 688245006969 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 688245006970 ATP Binding subdomain; other site 688245006971 Ligand Binding sites; other site 688245006972 Dimerization subdomain; other site 688245006973 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 688245006974 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 688245006975 Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate; Region: PCA_45_Dioxygenase_B; cd07364 688245006976 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 688245006977 active site 688245006978 Fe(II) binding site; other site 688245006979 dimer interface; other site 688245006980 tetramer interface; other site 688245006981 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cl06673 688245006982 dimer interface; other site 688245006983 tetramer interface; other site 688245006984 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 688245006985 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245006986 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 688245006987 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006988 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 688245006989 dimerization interface; other site 688245006990 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...; Region: Trunc_globin; cd00454 688245006991 apolar tunnel; other site 688245006992 heme binding site; other site 688245006993 dimerization interface; other site 688245006994 NnrS protein; Region: NnrS; cl01258 688245006995 Predicted transcriptional regulator [Transcription]; Region: COG1959 688245006996 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245006997 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 688245006998 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...; Region: FNR_like; cd00322 688245006999 FAD binding pocket; other site 688245007000 conserved FAD binding motif; other site 688245007001 phosphate binding motif; other site 688245007002 beta-alpha-beta structure motif; other site 688245007003 NAD binding pocket; other site 688245007004 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 688245007005 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245007006 Phage portal protein; Region: Phage_portal; cl01923 688245007007 terminase ATPase subunit; Provisional; Region: P; PHA02535 688245007008 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 688245007009 DNA binding site 688245007010 Int/Topo IB signature motif; other site 688245007011 active site 688245007012 Transposase DDE domain; Region: Transposase_11; pfam01609 688245007013 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 688245007014 synthetase active site; other site 688245007015 NTP binding site; other site 688245007016 metal-binding site 688245007017 integrase/recombinase; Provisional; Region: PRK15417 688245007018 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 a secondary target called the attC (or 59-base element)...; Region: INT_IntI; cd01193 688245007019 Int/Topo IB signature motif; other site 688245007020 conserved hypothetical protein TIGR02646; Region: TIGR02646 688245007021 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 688245007022 Q-loop/lid; other site 688245007023 ABC transporter signature motif; other site 688245007024 Walker B; other site 688245007025 D-loop; other site 688245007026 H-loop/switch region; other site 688245007027 haemagglutination activity domain; Region: Haemagg_act; cl05436 688245007028 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 688245007029 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245007030 Surface antigen; Region: Bac_surface_Ag; cl03097 688245007031 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 688245007032 short chain dehydrogenase; Provisional; Region: PRK06123 688245007033 classical (c) SDRs; Region: SDR_c; cd05233 688245007034 NAD(P) binding site; other site 688245007035 active site 688245007036 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 688245007037 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 688245007038 FAD binding pocket; other site 688245007039 FAD binding motif; other site 688245007040 phosphate binding motif; other site 688245007041 NAD binding pocket; other site 688245007042 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 688245007043 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245007044 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245007045 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 688245007046 N-terminal plug; other site 688245007047 ligand-binding site; other site 688245007048 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 688245007049 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245007050 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...; Region: AAA; cd00009 688245007051 Walker A motif; other site 688245007052 ATP binding site; other site 688245007053 Walker B motif; other site 688245007054 arginine finger; other site 688245007055 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 688245007056 Integrase core domain; Region: rve; cl01316 688245007057 potential frameshift: common BLAST hit: gi|168998487|ref|YP_001687757.1| transposase, IS4 family protein 688245007058 Transposase DDE domain; Region: Transposase_11; pfam01609 688245007059 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 688245007060 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 688245007061 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 688245007062 DNA binding residues 688245007063 dimer interface; other site 688245007064 putative metal binding site; other site 688245007065 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 688245007066 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 688245007067 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 688245007068 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 688245007069 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245007070 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; cl11391 688245007071 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 688245007072 lipoprotein signal peptidase; Provisional; Region: PRK14787 688245007073 Bacitracin resistance protein BacA; Region: BacA; cl00858 688245007074 Cytochrome c; Region: Cytochrom_C; cl11414 688245007075 Iron permease FTR1 family; Region: FTR1; cl00475 688245007076 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 688245007077 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 688245007078 Sulfatase; Region: Sulfatase; cl10460 688245007079 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 688245007080 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 688245007081 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 688245007082 Outer membrane efflux protein; Region: OEP; pfam02321 688245007083 Outer membrane efflux protein; Region: OEP; pfam02321 688245007084 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 688245007085 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 688245007086 active site 688245007087 phosphorylation site 688245007088 intermolecular recognition site; other site 688245007089 dimerization interface; other site 688245007090 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...; Region: trans_reg_C; cd00383 688245007091 DNA binding site 688245007092 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245007093 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 trans-...; Region: HisKA; cd00082 688245007094 dimer interface; other site 688245007095 phosphorylation site 688245007096 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 688245007097 ATP binding site; other site 688245007098 Mg2+ binding site; other site 688245007099 G-X-G motif; other site 688245007100 potential frameshift: common BLAST hit: gi|160898113|ref|YP_001563695.1| integrase catalytic region 688245007101 Integrase core domain; Region: rve; cl01316 688245007102 Domain of unknown function DUF; Region: DUF204; pfam02659 688245007103 Domain of unknown function DUF; Region: DUF204; pfam02659 688245007104 IS2 transposase TnpB; Reviewed; Region: PRK09409 688245007105 Integrase core domain; Region: rve; cl01316 688245007106 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; cl01116 688245007107 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 688245007108 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 688245007109 active site 688245007110 flagellar basal body rod protein FlgB; Provisional; Region: flgB; cl09471 688245007111 potential frameshift: common BLAST hit: gi|121593734|ref|YP_985630.1| heavy metal translocating P-type ATPase 688245007112 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245007113 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 688245007114 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; cl11391 688245007115 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 688245007116 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245007117 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 688245007118 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245007119 DNA binding residues 688245007120 Sulfatase; Region: Sulfatase; cl10460 688245007121 potential frameshift: common BLAST hit: gi|91788706|ref|YP_549658.1| transposase IS116/IS110/IS902 688245007122 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 688245007123 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 688245007124 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 688245007125 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 688245007126 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 688245007127 Outer membrane efflux protein; Region: OEP; pfam02321 688245007128 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 688245007129 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245007130 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245007131 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 trans-...; Region: HisKA; cd00082 688245007132 dimer interface; other site 688245007133 phosphorylation site 688245007134 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 688245007135 ATP binding site; other site 688245007136 Mg2+ binding site; other site 688245007137 G-X-G motif; other site 688245007138 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 688245007139 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 688245007140 active site 688245007141 phosphorylation site 688245007142 intermolecular recognition site; other site 688245007143 dimerization interface; other site 688245007144 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...; Region: trans_reg_C; cd00383 688245007145 DNA binding site 688245007146 Multicopper oxidase; Region: Cu-oxidase; cl14658 688245007147 Multicopper oxidase; Region: Cu-oxidase; cl14658 688245007148 Multicopper oxidase; Region: Cu-oxidase; cl14658 688245007149 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 688245007150 Copper resistance protein CopC; Region: CopC; cl01012 688245007151 Copper resistance protein D; Region: CopD; cl00563 688245007152 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 688245007153 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 688245007154 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245007155 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; cl11391 688245007156 Low molecular weight phosphatase family; Region: LMWPc; cd00115 688245007157 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 688245007158 active site 688245007159 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 688245007160 transmembrane helices; other site 688245007161 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 688245007162 catalytic residues; other site 688245007163 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245007164 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 688245007165 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 688245007166 Ligand Binding Site; other site 688245007167 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 688245007168 Permease family; Region: Xan_ur_permease; cl00967 688245007169 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 688245007170 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 688245007171 multiple promoter invertase; Provisional; Region: mpi; PRK13413 688245007172 catalytic residues; other site 688245007173 catalytic nucleophile; other site 688245007174 Presynaptic Site I dimer interface; other site 688245007175 Synaptic Antiparallel dimer interface; other site 688245007176 Synaptic Flat tetramer interface; other site 688245007177 Synaptic Site I dimer interface; other site 688245007178 DNA binding site 688245007179 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 688245007180 DNA-binding interface; DNA binding site 688245007181 Transposase; Region: Transposase_7; pfam01526 688245007182 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 688245007183 Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair]; Region: COG4644 688245007184 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245007185 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...; Region: AAA; cd00009 688245007186 Walker A motif; other site 688245007187 ATP binding site; other site 688245007188 Walker B motif; other site 688245007189 arginine finger; other site 688245007190 potential frameshift: common BLAST hit: gi|58616638|ref|YP_195847.1| transposase 688245007191 methyl-accepting chemotaxis protein II; Provisional; Region: PRK15048 688245007192 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 688245007193 putative active site; other site 688245007194 heme pocket; other site 688245007195 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 688245007196 Sensors of blue-light using FAD; Region: BLUF; pfam04940 688245007197 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 688245007198 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007199 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007200 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 688245007201 dimerization interface; other site 688245007202 allantoate amidohydrolase; Reviewed; Region: PRK12890 688245007203 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 688245007204 putative ADP-ribose binding site; other site 688245007205 putative active site; other site 688245007206 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...; Region: gram_neg_porins; cd00342 688245007207 trimer interface; other site 688245007208 eyelet of channel; other site 688245007209 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 688245007210 DinB family; Region: DinB; cl00986 688245007211 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 688245007212 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245007213 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 688245007214 DNA binding site 688245007215 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 688245007216 pyridoxal 5'-phosphate binding site; other site 688245007217 homodimer interface; other site 688245007218 catalytic residue; other site 688245007219 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 688245007220 putative substrate translocation pore; other site 688245007221 Beta-lactamase; Region: Beta-lactamase; cl01009 688245007222 potential frameshift: common BLAST hit: gi|226945638|ref|YP_002800711.1| Regulatory protein, LysR family 688245007223 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007224 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 688245007225 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 688245007226 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007227 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007228 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 688245007229 dimerization interface; other site 688245007230 atypical (a) SDRs, subgroup 3; Region: SDR_a3; cd05229 688245007231 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 688245007232 putative NAD(P) binding site; other site 688245007233 putative active site; other site 688245007234 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 688245007235 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245007236 DNA-binding transcriptional repressor LrhA; Provisional; Region: PRK15092 688245007237 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007238 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 688245007239 dimerization interface; other site 688245007240 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245007241 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245007242 potential frameshift: common BLAST hit: gi|167034315|ref|YP_001669546.1| luciferase family protein 688245007243 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 688245007244 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 688245007245 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 688245007246 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...; Region: GST_N_Ure2p_like; cd03048 688245007247 C-terminal domain interface; other site 688245007248 GSH binding site (G-site); other site 688245007249 dimer interface; other site 688245007250 GST_C 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...; Region: GST_C_Ure2p_like; cd03178 688245007251 dimer interface; other site 688245007252 N-terminal domain interface; other site 688245007253 putative substrate binding pocket (H-site); other site 688245007254 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245007255 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007256 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 688245007257 dimerization interface; other site 688245007258 substrate binding pocket; other site 688245007259 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245007260 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 688245007261 active site 688245007262 phosphorylation site 688245007263 intermolecular recognition site; other site 688245007264 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...; Region: LuxR_C_like; cd06170 688245007265 DNA binding residues 688245007266 dimerization interface; other site 688245007267 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 688245007268 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 688245007269 ATP binding site; other site 688245007270 Mg2+ binding site; other site 688245007271 G-X-G motif; other site 688245007272 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245007273 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 688245007274 active site 688245007275 phosphorylation site 688245007276 intermolecular recognition site; other site 688245007277 dimerization interface; other site 688245007278 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...; Region: LuxR_C_like; cd06170 688245007279 DNA binding residues 688245007280 dimerization interface; other site 688245007281 Fimbrial protein; Region: Fimbrial; cl01416 688245007282 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 688245007283 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 688245007284 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 688245007285 Fimbrial Usher protein; Region: Usher; pfam00577 688245007286 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 688245007287 Fimbrial protein; Region: Fimbrial; cl01416 688245007288 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245007289 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 688245007290 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 688245007291 Pyridoxine 5'-phosphate oxidase C-terminal dimerization region; Region: PNPOx_C; pfam10590 688245007292 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007293 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007294 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 688245007295 dimerization interface; other site 688245007296 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245007297 Coenzyme A binding pocket; other site 688245007298 Uncharacterized protein family (UPF0157); Region: UPF0157; cl00987 688245007299 Transposase DDE domain; Region: Transposase_11; pfam01609 688245007300 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 688245007301 homotrimer interaction site; other site 688245007302 putative active site; other site 688245007303 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 688245007304 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 688245007305 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245007306 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007307 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 688245007308 putative effector binding pocket; other site 688245007309 putative dimerization interface; other site 688245007310 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 688245007311 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; cl12031 688245007312 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 688245007313 atypical (a) SDRs, subgroup 6; Region: SDR_a6; cd05267 688245007314 putative NAD(P) binding site; other site 688245007315 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245007316 Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_4_FMN; cd04735 688245007317 putative active site; other site 688245007318 putative FMN binding site; other site 688245007319 putative substrate binding site; other site 688245007320 putative catalytic residue; other site 688245007321 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 688245007322 putative NAD(P) binding site; other site 688245007323 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 688245007324 NAD(P) binding site; other site 688245007325 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...; Region: gram_neg_porins; cd00342 688245007326 trimer interface; other site 688245007327 eyelet of channel; other site 688245007328 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 688245007329 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 688245007330 Integrase core domain; Region: rve; cl01316 688245007331 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245007332 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...; Region: AAA; cd00009 688245007333 Walker A motif; other site 688245007334 ATP binding site; other site 688245007335 Walker B motif; other site 688245007336 arginine finger; other site 688245007337 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...; Region: PBPb; cd00134 688245007338 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 688245007339 substrate binding pocket; other site 688245007340 membrane-bound complex binding site; other site 688245007341 hinge residues; other site 688245007342 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional; Region: PRK10841 688245007343 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 trans-...; Region: HisKA; cd00082 688245007344 dimer interface; other site 688245007345 phosphorylation site 688245007346 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 688245007347 ATP binding site; other site 688245007348 Mg2+ binding site; other site 688245007349 G-X-G motif; other site 688245007350 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 688245007351 active site 688245007352 phosphorylation site 688245007353 intermolecular recognition site; other site 688245007354 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 688245007355 active site 688245007356 phosphorylation site 688245007357 intermolecular recognition site; other site 688245007358 dimerization interface; other site 688245007359 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 688245007360 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional; Region: PRK10841 688245007361 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 trans-...; Region: HisKA; cd00082 688245007362 dimer interface; other site 688245007363 phosphorylation site 688245007364 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 688245007365 ATP binding site; other site 688245007366 Mg2+ binding site; other site 688245007367 G-X-G motif; other site 688245007368 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 688245007369 active site 688245007370 phosphorylation site 688245007371 intermolecular recognition site; other site 688245007372 dimerization interface; other site 688245007373 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; cl00086 688245007374 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007375 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245007376 Coenzyme A binding pocket; other site 688245007377 LysE type translocator; Region: LysE; cl00565 688245007378 EamA-like transporter family; Region: EamA; cl01037 688245007379 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007380 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007381 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 688245007382 dimerization interface; other site 688245007383 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 688245007384 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245007385 DNA binding site 688245007386 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 688245007387 pyridoxal 5'-phosphate binding site; other site 688245007388 homodimer interface; other site 688245007389 catalytic residue; other site 688245007390 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 688245007391 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007392 metal-binding site 688245007393 active site 688245007394 I-site; other site 688245007395 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 688245007396 conserved cys residue; other site 688245007397 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 688245007398 Autoinducer binding domain; Region: Autoind_bind; pfam03472 688245007399 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...; Region: LuxR_C_like; cd06170 688245007400 DNA binding residues 688245007401 dimerization interface; other site 688245007402 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245007403 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 688245007404 Protein of unknown function, DUF606; Region: DUF606; cl01273 688245007405 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007406 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007407 The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; Region: PBP2_ToxR; cd08465 688245007408 putative substrate binding pocket; other site 688245007409 putative dimerization interface; other site 688245007410 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 688245007411 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245007412 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007413 A new structural DNA glycosylase; Region: AlkD_like; cl11434 688245007414 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...; Region: S24_LexA-like; cd06529 688245007415 Catalytic site; other site 688245007416 Predicted ATP-binding protein involved in virulence [General function prediction only]; Region: COG3950 688245007417 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245007418 Q-loop/lid; other site 688245007419 ABC transporter signature motif; other site 688245007420 Walker B; other site 688245007421 D-loop; other site 688245007422 H-loop/switch region; other site 688245007423 Protein of unknown function (DUF1003); Region: DUF1003; cl01831 688245007424 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 688245007425 Ligand Binding Site; other site 688245007426 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 688245007427 Ligand Binding Site; other site 688245007428 Fimbrial protein; Region: Fimbrial; cl01416 688245007429 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007430 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007431 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 688245007432 dimerization interface; other site 688245007433 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245007434 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 688245007435 non-specific DNA binding site; other site 688245007436 salt bridge; other site 688245007437 sequence-specific DNA binding site; other site 688245007438 HipA-like N-terminal domain; Region: HipA_N; pfam07805 688245007439 HipA-like C-terminal domain; Region: HipA_C; pfam07804 688245007440 Fic/DOC family; Region: Fic; cl00960 688245007441 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 688245007442 Int/Topo IB signature motif; other site 688245007443 active site 688245007444 DNA binding site 688245007445 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 688245007446 Catalytic site; other site 688245007447 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 688245007448 RNA/DNA binding site; other site 688245007449 RRM dimerization site; other site 688245007450 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 688245007451 Predicted membrane protein [Function unknown]; Region: COG4129 688245007452 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 688245007453 Gas vesicle protein G; Region: GvpG; pfam05120 688245007454 Phage terminase large subunit; Region: Terminase_3; cl12054 688245007455 Protein of unknown function (DUF2829); Region: DUF2829; pfam11195 688245007456 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 688245007457 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 688245007458 S-adenosylmethionine binding site; other site 688245007459 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245007460 Protein of unknown function (DUF1064); Region: DUF1064; pfam06356 688245007461 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 688245007462 Phage antirepressor protein KilAC domain; Region: ANT; cl01462 688245007463 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 (...; Region: S24_LexA-like; cd06529 688245007464 Catalytic site; other site 688245007465 Putative exonuclease, RdgC; Region: RdgC; cl01122 688245007466 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 688245007467 Phage integrase family; Region: Phage_integrase; pfam00589 688245007468 DNA binding site 688245007469 Int/Topo IB signature motif; other site 688245007470 active site 688245007471 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl00696 688245007472 UbiA prenyltransferase family; Region: UbiA; cl00337 688245007473 Cytochrome c [Energy production and conversion]; Region: COG3258 688245007474 Cytochrome c; Region: Cytochrom_C; cl11414 688245007475 Cytochrome c; Region: Cytochrom_C; cl11414 688245007476 Cytochrome c; Region: Cytochrom_C; cl11414 688245007477 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245007478 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 688245007479 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245007480 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 trans-...; Region: HisKA; cd00082 688245007481 dimer interface; other site 688245007482 phosphorylation site 688245007483 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 688245007484 ATP binding site; other site 688245007485 Mg2+ binding site; other site 688245007486 G-X-G motif; other site 688245007487 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 688245007488 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 688245007489 active site 688245007490 phosphorylation site 688245007491 intermolecular recognition site; other site 688245007492 dimerization interface; other site 688245007493 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...; Region: trans_reg_C; cd00383 688245007494 DNA binding site 688245007495 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 688245007496 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...; Region: TlpA_like_family; cd02966 688245007497 catalytic residues; other site 688245007498 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 688245007499 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...; Region: DsbA_DsbC_DsbG; cd03020 688245007500 dimer interface; other site 688245007501 catalytic residues; other site 688245007502 DsrE/DsrF-like family; Region: DrsE; cl00672 688245007503 hypothetical protein; Provisional; Region: PRK10279 688245007504 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 688245007505 active site 688245007506 nucleophile elbow; other site 688245007507 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 688245007508 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 688245007509 nucleotide binding pocket; other site 688245007510 K-X-D-G motif; other site 688245007511 catalytic site; other site 688245007512 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 688245007513 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 688245007514 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 688245007515 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 688245007516 Dimer interface; other site 688245007517 BRCT sequence motif; other site 688245007518 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 688245007519 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 688245007520 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 688245007521 Walker A/P-loop; other site 688245007522 ATP binding site; other site 688245007523 Q-loop/lid; other site 688245007524 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 688245007525 ABC transporter signature motif; other site 688245007526 Walker B; other site 688245007527 D-loop; other site 688245007528 H-loop/switch region; other site 688245007529 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 688245007530 CHASE domain; Region: CHASE; cl01369 688245007531 PAS domain S-box; Region: sensory_box; TIGR00229 688245007532 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 688245007533 putative active site; other site 688245007534 heme pocket; other site 688245007535 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007536 metal-binding site 688245007537 active site 688245007538 I-site; other site 688245007539 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 688245007540 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 688245007541 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245007542 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245007543 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245007544 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 688245007545 Outer membrane efflux protein; Region: OEP; pfam02321 688245007546 Outer membrane efflux protein; Region: OEP; pfam02321 688245007547 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 688245007548 Protein export membrane protein; Region: SecD_SecF; cl14618 688245007549 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 688245007550 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 688245007551 putative substrate translocation pore; other site 688245007552 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 688245007553 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 688245007554 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 688245007555 putative substrate translocation pore; other site 688245007556 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 688245007557 hypothetical protein; Provisional; Region: PRK06194 688245007558 classical (c) SDRs; Region: SDR_c; cd05233 688245007559 NAD(P) binding site; other site 688245007560 active site 688245007561 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 688245007562 Prostaglandin dehydrogenases; Region: PGDH; cd05288 688245007563 NAD(P) binding site; other site 688245007564 substrate binding site; other site 688245007565 dimer interface; other site 688245007566 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 688245007567 CoenzymeA binding site; other site 688245007568 subunit interaction site; other site 688245007569 PHB binding site; other site 688245007570 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 688245007571 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007572 NAD(P) binding site; other site 688245007573 active site 688245007574 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 688245007575 DNA binding site 688245007576 active site 688245007577 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; cl12011 688245007578 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 688245007579 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 688245007580 nucleoside/Zn binding site; other site 688245007581 dimer interface; other site 688245007582 catalytic motif; other site 688245007583 putative cyanate transporter; Provisional; Region: cynX; PRK09705 688245007584 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245007585 Zn2+ binding site; other site 688245007586 UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: GlnD; COG2844 688245007587 Mg2+ binding site; other site 688245007588 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245007589 Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; Region: Adenylation_DNA_ligase_like; cl12015 688245007590 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 688245007591 phosphonate ABC transporter, periplasmic phosphonate binding protein; Region: PhnD; TIGR03431 688245007592 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 688245007593 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 688245007594 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 688245007595 Walker A/P-loop; other site 688245007596 ATP binding site; other site 688245007597 Q-loop/lid; other site 688245007598 ABC transporter signature motif; other site 688245007599 Walker B; other site 688245007600 D-loop; other site 688245007601 H-loop/switch region; other site 688245007602 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...; Region: TM_PBP2; cl00427 688245007603 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...; Region: TM_PBP2; cl00427 688245007604 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245007605 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007606 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 688245007607 Cytochrome c; Region: Cytochrom_C; cl11414 688245007608 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 688245007609 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 688245007610 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 688245007611 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245007612 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 trans-...; Region: HisKA; cd00082 688245007613 dimer interface; other site 688245007614 phosphorylation site 688245007615 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 688245007616 ATP binding site; other site 688245007617 Mg2+ binding site; other site 688245007618 G-X-G motif; other site 688245007619 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245007620 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 688245007621 active site 688245007622 phosphorylation site 688245007623 intermolecular recognition site; other site 688245007624 dimerization interface; other site 688245007625 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...; Region: trans_reg_C; cd00383 688245007626 DNA binding site 688245007627 SelR domain; Region: SelR; cl00369 688245007628 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 688245007629 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 688245007630 catalytic residues; other site 688245007631 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 688245007632 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245007633 Proteobacterial; Region: dnaQ_proteo; TIGR01406 688245007634 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 688245007635 catalytic loop; other site 688245007636 iron binding site; other site 688245007637 chaperone protein HscA; Provisional; Region: hscA; PRK05183 688245007638 co-chaperone HscB; Provisional; Region: hscB; PRK03578 688245007639 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...; Region: DnaJ; cl02542 688245007640 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 688245007641 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 688245007642 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 688245007643 trimerization site; other site 688245007644 active site 688245007645 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 688245007646 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 688245007647 pyridoxal 5'-phosphate binding pocket; other site 688245007648 catalytic residue; other site 688245007649 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007650 rrf2 family protein (putative transcriptional regulator); Region: rrf2_super; TIGR00738 688245007651 excinuclease ABC subunit B; Provisional; Region: PRK05298 688245007652 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 688245007653 ATP binding site; other site 688245007654 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 688245007655 nucleotide binding region; other site 688245007656 ATP-binding site; other site 688245007657 Ultra-violet resistance protein B; Region: UvrB; pfam12344 688245007658 UvrB/uvrC motif; Region: UVR; pfam02151 688245007659 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 688245007660 pyridoxal 5'-phosphate binding site; other site 688245007661 homodimer interface; other site 688245007662 catalytic residue; other site 688245007663 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 688245007664 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 688245007665 putative active site; other site 688245007666 metal-binding site 688245007667 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245007668 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...; Region: Aldo_ket_red; cd06660 688245007669 active site 688245007670 catalytic tetrad; other site 688245007671 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 688245007672 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007673 Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate; Region: PCA_45_Dioxygenase_B; cd07364 688245007674 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 688245007675 active site 688245007676 Fe(II) binding site; other site 688245007677 dimer interface; other site 688245007678 tetramer interface; other site 688245007679 The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit; Region: PCA_45_Doxase_A; cd07924 688245007680 tetramer interface; other site 688245007681 dimer interface; other site 688245007682 active site 688245007683 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 688245007684 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 688245007685 active site 688245007686 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 688245007687 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...; Region: metallo-dependent_hydrolases; cl00281 688245007688 benzoate transport; Region: 2A0115; TIGR00895 688245007689 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 688245007690 putative substrate translocation pore; other site 688245007691 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 688245007692 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 688245007693 Cytochrome P450; Region: p450; cl12078 688245007694 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 688245007695 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 688245007696 Glycosyltransferase family 29 (sialyltransferase); Region: Glyco_transf_29; pfam00777 688245007697 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 688245007698 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 688245007699 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 688245007700 active site 688245007701 dimer interface; other site 688245007702 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 688245007703 dimer interface; other site 688245007704 active site 688245007705 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 688245007706 active site 688245007707 tetramer interface; other site 688245007708 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007709 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 688245007710 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 688245007711 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 688245007712 Cupin domain; Region: Cupin_2; cl09118 688245007713 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 688245007714 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 688245007715 substrate binding site; other site 688245007716 tetramer interface; other site 688245007717 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 688245007718 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 688245007719 NADP binding site; other site 688245007720 active site 688245007721 putative substrate binding site; other site 688245007722 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 688245007723 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 688245007724 NAD binding site; other site 688245007725 substrate binding site; other site 688245007726 homodimer interface; other site 688245007727 active site 688245007728 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 688245007729 Rhamnan synthesis protein F; Region: RgpF; cl01529 688245007730 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 688245007731 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 688245007732 active site 688245007733 Transposase DDE domain; Region: Transposase_11; pfam01609 688245007734 Rhamnan synthesis protein F; Region: RgpF; cl01529 688245007735 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 688245007736 Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis; Region: GT2_RfbC_Mx_like; cd04184 688245007737 Probable Catalytic site; other site 688245007738 metal-binding site 688245007739 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 688245007740 Probable Catalytic site; other site 688245007741 metal-binding site 688245007742 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 688245007743 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 688245007744 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 688245007745 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 688245007746 Vi polysaccharide export inner membrane protein VexD; Provisional; Region: PRK15178 688245007747 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245007748 Q-loop/lid; other site 688245007749 ABC transporter signature motif; other site 688245007750 Walker B; other site 688245007751 D-loop; other site 688245007752 H-loop/switch region; other site 688245007753 ABC-2 type transporter; Region: ABC2_membrane; cl11417 688245007754 selenophosphate synthetase; Provisional; Region: PRK00943 688245007755 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 688245007756 dimerization interface; other site 688245007757 putative ATP binding site; other site 688245007758 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245007759 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007760 Domain of unknown function (DUF74); Region: DUF74; cl00426 688245007761 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245007762 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007763 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 688245007764 dimerization interface; other site 688245007765 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245007766 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007767 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3435 688245007768 Cupin domain; Region: Cupin_2; cl09118 688245007769 Cupin domain; Region: Cupin_2; cl09118 688245007770 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245007771 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 688245007772 maleylacetoacetate isomerase; Region: maiA; TIGR01262 688245007773 C-terminal domain interface; other site 688245007774 GSH binding site (G-site); other site 688245007775 putative dimer interface; other site 688245007776 GST_C 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_C_Zeta; cd03191 688245007777 dimer interface; other site 688245007778 N-terminal domain interface; other site 688245007779 putative maleylacetoacetate (MAA) substrate binding site (H site); other site 688245007780 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 688245007781 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 688245007782 tetrameric interface; other site 688245007783 NAD binding site; other site 688245007784 catalytic residues; other site 688245007785 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 688245007786 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 688245007787 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245007788 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245007789 active site 688245007790 Protein of unknown function, DUF488; Region: DUF488; cl01246 688245007791 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007792 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 688245007793 Cupin domain; Region: Cupin_2; cl09118 688245007794 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007795 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 688245007796 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 688245007797 tetrameric interface; other site 688245007798 NAD binding site; other site 688245007799 catalytic residues; other site 688245007800 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007801 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245007802 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 688245007803 dimerization interface; other site 688245007804 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245007805 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245007806 active site 688245007807 Cupin domain; Region: Cupin_2; cl09118 688245007808 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245007809 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 688245007810 Cupin domain; Region: Cupin_2; cl09118 688245007811 potential frameshift: common BLAST hit: gi|160899103|ref|YP_001564685.1| transcriptional regulator 688245007812 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 688245007813 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245007814 DNA binding site 688245007815 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 688245007816 pyridoxal 5'-phosphate binding site; other site 688245007817 LysE type translocator; Region: LysE; cl00565 688245007818 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245007819 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 688245007820 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 688245007821 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 688245007822 active site residue 688245007823 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 688245007824 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 688245007825 catalytic motif; other site 688245007826 Catalytic residue; other site 688245007827 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 688245007828 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 688245007829 catalytic residues; other site 688245007830 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 688245007831 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 688245007832 Trp docking motif; other site 688245007833 active site 688245007834 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 688245007835 'Velcro' closure; other site 688245007836 isocitrate dehydrogenase; Validated; Region: PRK07362 688245007837 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 688245007838 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 688245007839 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; cl12031 688245007840 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245007841 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 688245007842 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245007843 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 688245007844 Monomeric isocitrate dehydrogenase; Region: IDH; pfam03971 688245007845 H-NS histone family; Region: Histone_HNS; pfam00816 688245007846 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 688245007847 CHASE3 domain; Region: CHASE3; cl05000 688245007848 PAS fold; Region: PAS_4; pfam08448 688245007849 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 688245007850 putative active site; other site 688245007851 heme pocket; other site 688245007852 PAS fold; Region: PAS_4; pfam08448 688245007853 bacterio-opsin activator; Provisional; Region: PRK13558 688245007854 GAF domain; Region: GAF; cl00853 688245007855 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007856 metal-binding site 688245007857 active site 688245007858 I-site; other site 688245007859 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 688245007860 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 688245007861 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 688245007862 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 688245007863 putative active site; other site 688245007864 metal-binding site 688245007865 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 688245007866 superoxide dismutase; Provisional; Region: PRK10543 688245007867 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 688245007868 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 688245007869 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 single-strand-...; Region: ExoVII_LU_OBF; cd04489 688245007870 generic binding surface II; other site 688245007871 generic binding surface I; other site 688245007872 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 688245007873 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 688245007874 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 688245007875 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 688245007876 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 688245007877 putative hydrophobic ligand binding site; other site 688245007878 CHAD domain; Region: CHAD; cl10506 688245007879 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...; Region: Aldo_ket_red; cd06660 688245007880 active site 688245007881 catalytic tetrad; other site 688245007882 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 688245007883 dimerization interface; other site 688245007884 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; cl09110 688245007885 Citrate transporter; Region: CitMHS; pfam03600 688245007886 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 688245007887 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 688245007888 Trm112p-like protein; Region: Trm112p; cl01066 688245007889 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 688245007890 Ligand binding site; other site 688245007891 oligomer interface; other site 688245007892 adenylate kinase; Reviewed; Region: adk; PRK00279 688245007893 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 688245007894 AMP-binding site; other site 688245007895 ATP-AMP (Ap5A)-binding site; other site 688245007896 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cl00216 688245007897 active site/substrate binding site 688245007898 tetramer interface; other site 688245007899 LexA repressor; Validated; Region: PRK00215 688245007900 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007901 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 (...; Region: S24_LexA-like; cd06529 688245007902 Catalytic site; other site 688245007903 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 688245007904 Ligand Binding Site; other site 688245007905 nitrobindin heme-binding domain; Region: nitrobindin; cd07828 688245007906 heme-binding site; other site 688245007907 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 688245007908 Ligand Binding Site; other site 688245007909 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...; Region: metallo-dependent_hydrolases; cl00281 688245007910 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 688245007911 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 688245007912 active site 688245007913 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 688245007914 Cupin domain; Region: Cupin_2; cl09118 688245007915 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 688245007916 Domain of unknown function (DUF333); Region: DUF333; pfam03891 688245007917 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007918 metal-binding site 688245007919 active site 688245007920 I-site; other site 688245007921 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 688245007922 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007923 metal-binding site 688245007924 active site 688245007925 I-site; other site 688245007926 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 688245007927 PAS fold; Region: PAS_4; pfam08448 688245007928 putative active site; other site 688245007929 heme pocket; other site 688245007930 PAS domain S-box; Region: sensory_box; TIGR00229 688245007931 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 688245007932 putative active site; other site 688245007933 heme pocket; other site 688245007934 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245007935 metal-binding site 688245007936 active site 688245007937 I-site; other site 688245007938 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 688245007939 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245007940 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 688245007941 multifunctional aminopeptidase A; Provisional; Region: PRK00913 688245007942 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...; Region: Peptidase_M17; cd00433 688245007943 interface (dimer of trimers); other site 688245007944 Substrate-binding/catalytic site; other site 688245007945 Zn-binding sites; other site 688245007946 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 688245007947 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 688245007948 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...; Region: CbiX_SirB_N; cd03416 688245007949 putative active site; other site 688245007950 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 688245007951 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245007952 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 688245007953 substrate binding site; other site 688245007954 dimerization interface; other site 688245007955 methionine aminotransferase; Validated; Region: PRK09082 688245007956 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 688245007957 pyridoxal 5'-phosphate binding site; other site 688245007958 homodimer interface; other site 688245007959 catalytic residue; other site 688245007960 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 688245007961 active site 688245007962 metal-binding site 688245007963 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 688245007964 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 688245007965 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 688245007966 Cytochrome c; Region: Cytochrom_C; cl11414 688245007967 Cytochrome c; Region: Cytochrom_C; cl11414 688245007968 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 688245007969 Moco binding site; other site 688245007970 metal coordination site; other site 688245007971 Cytochrome c; Region: Cytochrom_C; cl11414 688245007972 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 688245007973 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245007974 DsrE/DsrF-like family; Region: DrsE; cl00672 688245007975 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 688245007976 dimerization interface; other site 688245007977 putative DNA binding site; other site 688245007978 putative Zn2+ binding site; other site 688245007979 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...; Region: ADPRase_NUDT5; cd03424 688245007980 dimer interface; other site 688245007981 ADP-ribose binding site; other site 688245007982 active site 688245007983 nudix motif; other site 688245007984 metal-binding site 688245007985 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245007986 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245007987 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 688245007988 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245007989 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 688245007990 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245007991 substrate binding pocket; other site 688245007992 active site 688245007993 iron coordination sites; other site 688245007994 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; cl12031 688245007995 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 688245007996 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...; Region: gram_neg_porins; cd00342 688245007997 trimer interface; other site 688245007998 eyelet of channel; other site 688245007999 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)...; Region: Rieske; cl00938 688245008000 iron-sulfur cluster; other site 688245008001 [2Fe-2S] cluster binding site; other site 688245008002 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 688245008003 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 688245008004 catalytic residues; other site 688245008005 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 688245008006 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 688245008007 NADP binding site; other site 688245008008 dimer interface; other site 688245008009 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 688245008010 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 688245008011 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245008012 active site 688245008013 ribonuclease G; Provisional; Region: PRK11712 688245008014 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 688245008015 homodimer interface; other site 688245008016 oligonucleotide binding site; other site 688245008017 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 688245008018 active site 688245008019 dimer interface; other site 688245008020 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 688245008021 Domain of unknown function DUF143; Region: DUF143; cl00519 688245008022 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 688245008023 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 688245008024 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 688245008025 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245008026 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 688245008027 Domain of unknown function DUF28; Region: DUF28; cl00361 688245008028 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245008029 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 688245008030 Walker A motif; other site 688245008031 ATP binding site; other site 688245008032 potential frameshift: common BLAST hit: gi|160898914|ref|YP_001564496.1| methyl-accepting chemotaxis sensory transducer 688245008033 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245008034 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245008035 enoyl-CoA hydratase; Provisional; Region: PRK06142 688245008036 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 688245008037 substrate binding site; other site 688245008038 oxyanion hole (OAH) forming residues; other site 688245008039 trimer interface; other site 688245008040 serine racemase; Region: PLN02970 688245008041 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 688245008042 tetramer interface; other site 688245008043 pyridoxal 5'-phosphate binding site; other site 688245008044 catalytic residue; other site 688245008045 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245008046 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 688245008047 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 688245008048 potential catalytic triad; other site 688245008049 conserved cys residue; other site 688245008050 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245008051 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 688245008052 DNA binding residues 688245008053 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008054 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 688245008055 NAD(P) binding site; other site 688245008056 active site 688245008057 Domain of unknown function DUF28; Region: DUF28; cl00361 688245008058 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 688245008059 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 688245008060 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 688245008061 Nucleoside recognition; Region: Gate; cl00486 688245008062 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245008063 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...; Region: PBPb; cd00134 688245008064 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245008065 substrate binding pocket; other site 688245008066 membrane-bound complex binding site; other site 688245008067 hinge residues; other site 688245008068 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 688245008069 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008070 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008071 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 688245008072 putative dimerization interface; other site 688245008073 exonuclease I; Provisional; Region: sbcB; PRK11779 688245008074 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 688245008075 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 688245008076 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 688245008077 Membrane transport protein; Region: Mem_trans; cl09117 688245008078 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245008079 dimerization interface; other site 688245008080 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245008081 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245008082 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 688245008083 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 688245008084 conserved cys residue; other site 688245008085 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 688245008086 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008087 NAD(P) binding site; other site 688245008088 active site 688245008089 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 688245008090 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 688245008091 dimer interface; other site 688245008092 active site 688245008093 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 688245008094 CoenzymeA binding site; other site 688245008095 subunit interaction site; other site 688245008096 PHB binding site; other site 688245008097 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein...; Region: SIRT4; cd01409 688245008098 NAD+ binding site; other site 688245008099 substrate binding site; other site 688245008100 Zn binding site; other site 688245008101 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 688245008102 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245008103 active site 688245008104 signature motif; other site 688245008105 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245008106 active site 688245008107 signature motif; other site 688245008108 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 688245008109 non-specific DNA binding site; other site 688245008110 salt bridge; other site 688245008111 sequence-specific DNA binding site; other site 688245008112 GAF domain; Region: GAF; cl00853 688245008113 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 688245008114 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245008115 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245008116 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 688245008117 d-galactonate transporter; Region: 2A0114; TIGR00893 688245008118 putative substrate translocation pore; other site 688245008119 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 688245008120 Beta-lactamase; Region: Beta-lactamase; cl01009 688245008121 dihydropyrimidinase; Provisional; Region: PRK13404 688245008122 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like...; Region: D-HYD; cd01314 688245008123 tetramer interface; other site 688245008124 active site 688245008125 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245008126 Transcriptional regulators [Transcription]; Region: FadR; COG2186 688245008127 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245008128 DNA binding site 688245008129 FCD domain; Region: FCD; cl11656 688245008130 Chromate transporter; Region: Chromate_transp; cl00902 688245008131 Chromate transporter; Region: Chromate_transp; cl00902 688245008132 NAD-dependent deacetylase; Provisional; Region: PRK14138 688245008133 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes...; Region: SIRT5_Af1_CobB; cd01412 688245008134 NAD+ binding site; other site 688245008135 substrate binding site; other site 688245008136 Zn binding site; other site 688245008137 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 688245008138 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 688245008139 putative active site; other site 688245008140 heme pocket; other site 688245008141 sensory histidine kinase AtoS; Provisional; Region: PRK11360 688245008142 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 688245008143 ATP binding site; other site 688245008144 Mg2+ binding site; other site 688245008145 G-X-G motif; other site 688245008146 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 688245008147 active site 688245008148 phosphorylation site 688245008149 intermolecular recognition site; other site 688245008150 dimerization interface; other site 688245008151 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 688245008152 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 688245008153 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 688245008154 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 688245008155 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 688245008156 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 688245008157 Walker A/P-loop; other site 688245008158 ATP binding site; other site 688245008159 Q-loop/lid; other site 688245008160 ABC transporter signature motif; other site 688245008161 Walker B; other site 688245008162 D-loop; other site 688245008163 H-loop/switch region; other site 688245008164 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 688245008165 active site 688245008166 catalytic triad; other site 688245008167 oxyanion hole; other site 688245008168 switch loop; other site 688245008169 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 688245008170 cystathionine beta-lyase; Provisional; Region: PRK07050 688245008171 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 688245008172 pyridoxal 5'-phosphate binding pocket; other site 688245008173 catalytic residue; other site 688245008174 Putative phospholipid-binding domain; Region: BON; cl02771 688245008175 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245008176 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 688245008177 putative substrate translocation pore; other site 688245008178 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 688245008179 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 688245008180 nucleophile elbow; other site 688245008181 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 688245008182 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 688245008183 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245008184 active site 688245008185 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 688245008186 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 688245008187 dimer interface; other site 688245008188 active site 688245008189 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 688245008190 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 688245008191 substrate binding site; other site 688245008192 oxyanion hole (OAH) forming residues; other site 688245008193 trimer interface; other site 688245008194 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008195 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245008196 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245008197 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245008198 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245008199 Walker A/P-loop; other site 688245008200 ATP binding site; other site 688245008201 Q-loop/lid; other site 688245008202 ABC transporter signature motif; other site 688245008203 Walker B; other site 688245008204 D-loop; other site 688245008205 H-loop/switch region; other site 688245008206 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245008207 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245008208 Walker A/P-loop; other site 688245008209 ATP binding site; other site 688245008210 Q-loop/lid; other site 688245008211 ABC transporter signature motif; other site 688245008212 Walker B; other site 688245008213 D-loop; other site 688245008214 H-loop/switch region; other site 688245008215 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 688245008216 TM-ABC transporter signature motif; other site 688245008217 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 688245008218 TM-ABC transporter signature motif; other site 688245008219 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245008220 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 688245008221 putative ligand binding site; other site 688245008222 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245008223 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 688245008224 putative ligand binding site; other site 688245008225 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245008226 putative acyl-CoA synthetase; Provisional; Region: PRK06018 688245008227 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; cl00428 688245008228 SelR domain; Region: SelR; cl00369 688245008229 Intracellular septation protein A; Region: IspA; cl01098 688245008230 BolA-like protein; Region: BolA; cl00386 688245008231 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 688245008232 PPIC-type PPIASE domain; Region: Rotamase; cl08278 688245008233 RNA polymerase sigma factor; Provisional; Region: PRK12513 688245008234 Sodium:solute symporter family; Region: SSF; cl00456 688245008235 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 688245008236 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 688245008237 Bacterial SH3 domain; Region: SH3_3; cl02551 688245008238 Bacterial SH3 domain; Region: SH3_3; cl02551 688245008239 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 688245008240 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 688245008241 dimer interface; other site 688245008242 substrate binding site; other site 688245008243 ATP binding site; other site 688245008244 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008245 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 688245008246 thiS-thiF/thiG interaction site; other site 688245008247 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 688245008248 ThiS interaction site; other site 688245008249 putative active site; other site 688245008250 tetramer interface; other site 688245008251 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- (beta...; Region: TMP_TenI; cd00564 688245008252 active site 688245008253 thiamine phosphate binding site; other site 688245008254 pyrophosphate binding site; other site 688245008255 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245008256 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 688245008257 ligand binding site; other site 688245008258 flexible hinge region; other site 688245008259 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 688245008260 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 688245008261 putative active site; other site 688245008262 putative substrate binding site; other site 688245008263 ATP binding site; other site 688245008264 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245008265 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245008266 active site 688245008267 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245008268 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245008269 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245008270 peptide chain release factor 2; Provisional; Region: PRK08787 688245008271 RF-1 domain; Region: RF-1; cl02875 688245008272 RF-1 domain; Region: RF-1; cl02875 688245008273 aminopeptidase N; Provisional; Region: pepN; PRK14015 688245008274 Peptidase family M1; Region: Peptidase_M1; pfam01433 688245008275 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-1,7-...; Region: FBPase; cd00354 688245008276 AMP binding site; other site 688245008277 metal-binding site 688245008278 active site 688245008279 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 688245008280 catalytic residue; other site 688245008281 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 688245008282 Domain of unknown function (DUF927); Region: DUF927; cl12098 688245008283 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 688245008284 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245008285 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 688245008286 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 688245008287 Int/Topo IB signature motif; other site 688245008288 active site 688245008289 DNA binding site 688245008290 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 688245008291 rRNA binding site; other site 688245008292 predicted 30S ribosome binding site; other site 688245008293 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 688245008294 Cache domain; Region: Cache_1; pfam02743 688245008295 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245008296 metal-binding site 688245008297 active site 688245008298 I-site; other site 688245008299 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008300 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008301 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 688245008302 putative dimerization interface; other site 688245008303 Membrane transport protein; Region: Mem_trans; cl09117 688245008304 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245008305 active site 688245008306 I-site; other site 688245008307 metal-binding site 688245008308 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 688245008309 Bacterial protein of unknown function (DUF920); Region: DUF920; cl01479 688245008310 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 688245008311 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 688245008312 metal ion-dependent adhesion site (MIDAS); other site 688245008313 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; cl12108 688245008314 VCBS repeat; Region: VCBS_repeat; TIGR01965 688245008315 VCBS repeat; Region: VCBS_repeat; TIGR01965 688245008316 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cl02468 688245008317 Ca2+ binding site; other site 688245008318 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245008319 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...; Region: LuxR_C_like; cd06170 688245008320 DNA binding residues 688245008321 dimerization interface; other site 688245008322 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 688245008323 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 688245008324 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 688245008325 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245008326 ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two...; Region: ABCC_bacteriocin_exporters; cd03245 688245008327 Walker A/P-loop; other site 688245008328 ATP binding site; other site 688245008329 Q-loop/lid; other site 688245008330 ABC transporter signature motif; other site 688245008331 Walker B; other site 688245008332 D-loop; other site 688245008333 H-loop/switch region; other site 688245008334 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 688245008335 Outer membrane efflux protein; Region: OEP; pfam02321 688245008336 Outer membrane efflux protein; Region: OEP; pfam02321 688245008337 Transposase DDE domain; Region: Transposase_11; pfam01609 688245008338 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 688245008339 DNA binding residues 688245008340 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 higher...; Region: HU_IHF; cd00591 688245008341 IHF dimer interface; other site 688245008342 IHF - DNA interface; other site 688245008343 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 688245008344 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 688245008345 putative tRNA-binding site; other site 688245008346 B3/4 domain; Region: B3_4; cl11458 688245008347 tRNA synthetase B5 domain; Region: B5; cl08394 688245008348 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 688245008349 dimer interface; other site 688245008350 motif 1; other site 688245008351 motif 3; other site 688245008352 motif 2; other site 688245008353 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 688245008354 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 688245008355 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 688245008356 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 688245008357 dimer interface; other site 688245008358 motif 1; other site 688245008359 active site 688245008360 motif 2; other site 688245008361 motif 3; other site 688245008362 Ribosomal protein L20; Region: Ribosomal_L20; cl00393 688245008363 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 688245008364 translation initiation factor IF-3; Region: infC; TIGR00168 688245008365 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 688245008366 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 688245008367 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 688245008368 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...; Region: TGS_ThrRS_N; cd01667 688245008369 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 688245008370 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 688245008371 active site 688245008372 dimer interface; other site 688245008373 motif 1; other site 688245008374 motif 2; other site 688245008375 motif 3; other site 688245008376 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 688245008377 anticodon binding site; other site 688245008378 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 688245008379 tetramer interface; other site 688245008380 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 688245008381 active site 688245008382 Mg2+/Mn2+ binding site; other site 688245008383 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 688245008384 EamA-like transporter family; Region: EamA; cl01037 688245008385 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 688245008386 SWIB/MDM2 domain; Region: SWIB; cl02489 688245008387 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 688245008388 non-specific DNA binding site; other site 688245008389 salt bridge; other site 688245008390 sequence-specific DNA binding site; other site 688245008391 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245008392 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245008393 ferredoxin--NADP+ reductase; Provisional; Region: PLN03116 688245008394 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 688245008395 FAD binding pocket; other site 688245008396 FAD binding motif; other site 688245008397 catalytic residues; other site 688245008398 NAD binding pocket; other site 688245008399 phosphate binding motif; other site 688245008400 beta-alpha-beta structure motif; other site 688245008401 ApbE family; Region: ApbE; cl00643 688245008402 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 688245008403 ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CbiK; COG5266 688245008404 Predicted periplasmic protein (DUF2271); Region: DUF2271; cl01469 688245008405 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 688245008406 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 688245008407 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 688245008408 N-terminal plug; other site 688245008409 ligand-binding site; other site 688245008410 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245008411 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 688245008412 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 688245008413 active site 688245008414 substrate binding site; other site 688245008415 FMN binding site; other site 688245008416 putative catalytic residues; other site 688245008417 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 688245008418 Gram-negative bacterial tonB protein; Region: TonB; cl10048 688245008419 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 688245008420 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 688245008421 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 688245008422 Hemin uptake protein hemP; Region: hemP; cl10043 688245008423 Domain of unknown function (DUF336); Region: DUF336; cl01249 688245008424 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 688245008425 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 688245008426 superoxide dismutase; Provisional; Region: PRK10925 688245008427 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 688245008428 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 688245008429 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 688245008430 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 688245008431 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; cl12011 688245008432 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008433 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 688245008434 putative NAD(P) binding site; other site 688245008435 active site 688245008436 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 688245008437 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 688245008438 putative active site; other site 688245008439 heme pocket; other site 688245008440 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245008441 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245008442 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 688245008443 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008444 Proline dehydrogenase; Region: Pro_dh; cl03282 688245008445 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 688245008446 NAD(P) binding site; other site 688245008447 catalytic residues; other site 688245008448 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 688245008449 TOBE domain; Region: TOBE_2; cl01440 688245008450 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 688245008451 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008452 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 688245008453 substrate binding site; other site 688245008454 dimerization interface; other site 688245008455 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 688245008456 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245008457 Walker A/P-loop; other site 688245008458 ATP binding site; other site 688245008459 Q-loop/lid; other site 688245008460 ABC transporter signature motif; other site 688245008461 Walker B; other site 688245008462 D-loop; other site 688245008463 H-loop/switch region; other site 688245008464 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...; Region: TM_PBP2; cd06261 688245008465 putative PBP binding loops; other site 688245008466 dimer interface; other site 688245008467 ABC-ATPase subunit interface; other site 688245008468 potential frameshift: common BLAST hit: gi|160900070|ref|YP_001565652.1| alkanesulfonate monooxygenase 688245008469 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 688245008470 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 688245008471 active site 688245008472 probable F420-dependent oxidoreductase, Rv2161c family; Region: F420_Rv2161c; TIGR03619 688245008473 dimer interface; other site 688245008474 non-prolyl cis peptide bond; other site 688245008475 insertion regions; other site 688245008476 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 688245008477 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...; Region: PBPb; cd00134 688245008478 substrate binding pocket; other site 688245008479 membrane-bound complex binding site; other site 688245008480 hinge residues; other site 688245008481 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 688245008482 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...; Region: PBPb; cd00134 688245008483 substrate binding pocket; other site 688245008484 membrane-bound complex binding site; other site 688245008485 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245008486 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 688245008487 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 688245008488 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245008489 metal-binding site 688245008490 active site 688245008491 I-site; other site 688245008492 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245008493 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008494 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 688245008495 dimerization interface; other site 688245008496 substrate binding pocket; other site 688245008497 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...; Region: Aldo_ket_red; cd06660 688245008498 active site 688245008499 catalytic tetrad; other site 688245008500 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 688245008501 putative hydrophobic ligand binding site; other site 688245008502 protein interface; other site 688245008503 gate; other site 688245008504 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...; Region: metallo-dependent_hydrolases; cl00281 688245008505 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 688245008506 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 688245008507 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; cl09108 688245008508 phosphate binding site; other site 688245008509 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 688245008510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008511 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 688245008512 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245008513 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 688245008514 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 688245008515 enoyl-CoA hydratase; Provisional; Region: PRK06127 688245008516 substrate binding site; other site 688245008517 oxyanion hole (OAH) forming residues; other site 688245008518 trimer interface; other site 688245008519 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245008520 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 688245008521 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...; Region: metallo-dependent_hydrolases; cl00281 688245008522 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245008523 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008524 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 688245008525 dimerization interface; other site 688245008526 substrate binding pocket; other site 688245008527 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 688245008528 dimer interface; other site 688245008529 NADP binding site; other site 688245008530 catalytic residues; other site 688245008531 metabolite-proton symporter; Region: 2A0106; TIGR00883 688245008532 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 688245008533 putative substrate translocation pore; other site 688245008534 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 688245008535 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 688245008536 putative active site; other site 688245008537 metal-binding site 688245008538 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008539 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245008540 DctM-like transporters; Region: DctM; pfam06808 688245008541 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; cl09110 688245008542 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245008543 NIPSNAP; Region: NIPSNAP; pfam07978 688245008544 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 688245008545 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 688245008546 active site 688245008547 NAD binding site; other site 688245008548 metal-binding site 688245008549 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008550 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008551 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 688245008552 dimerization interface; other site 688245008553 Phenolic acid decarboxylase (PAD); Region: PA_decarbox; cl01382 688245008554 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...; Region: Aldo_ket_red; cd06660 688245008555 active site 688245008556 catalytic tetrad; other site 688245008557 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 688245008558 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 688245008559 FMN binding site; other site 688245008560 active site 688245008561 substrate binding site; other site 688245008562 catalytic residue; other site 688245008563 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 688245008564 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 688245008565 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...; Region: Aldo_ket_red; cd06660 688245008566 active site 688245008567 catalytic tetrad; other site 688245008568 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 688245008569 putative substrate translocation pore; other site 688245008570 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 688245008571 putative substrate translocation pore; other site 688245008572 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008573 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008574 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 688245008575 putative effector binding pocket; other site 688245008576 dimerization interface; other site 688245008577 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 688245008578 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 688245008579 DNA binding residues 688245008580 dimer interface; other site 688245008581 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008582 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 688245008583 NAD(P) binding site; other site 688245008584 active site 688245008585 Uncharacterized conserved protein [Function unknown]; Region: COG2128 688245008586 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008587 C-term; Region: GreA_GreB; pfam01272 688245008588 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 688245008589 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 688245008590 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245008591 DNA binding site 688245008592 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 688245008593 pyridoxal 5'-phosphate binding site; other site 688245008594 homodimer interface; other site 688245008595 catalytic residue; other site 688245008596 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 688245008597 homodimer interface; other site 688245008598 NAD binding site; other site 688245008599 catalytic residues; other site 688245008600 substrate binding pocket; other site 688245008601 flexible flap; other site 688245008602 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 688245008603 active site 688245008604 catalytic residues; other site 688245008605 metal-binding site 688245008606 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 688245008607 Secretin and TonB N terminus short domain; Region: STN; pfam07660 688245008608 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245008609 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 688245008610 N-terminal plug; other site 688245008611 ligand-binding site; other site 688245008612 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 688245008613 FecR protein; Region: FecR; pfam04773 688245008614 RNA polymerase sigma factor; Reviewed; Region: PRK12527 688245008615 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...; Region: Sigma70_r4; cl01055 688245008616 Cupin domain; Region: Cupin_2; cl09118 688245008617 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245008618 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245008619 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 688245008620 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 688245008621 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 688245008622 dimer interface; other site 688245008623 active site 688245008624 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245008625 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245008626 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 688245008627 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...; Region: gram_neg_porins; cd00342 688245008628 trimer interface; other site 688245008629 eyelet of channel; other site 688245008630 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008631 FAD binding domain; Region: FAD_binding_3; pfam01494 688245008632 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245008633 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008634 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 688245008635 dimerization interface; other site 688245008636 putative effector binding pocket; other site 688245008637 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 688245008638 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008639 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245008640 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 688245008641 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245008642 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 688245008643 catalytic residues; other site 688245008644 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 688245008645 transmembrane helices; other site 688245008646 Low molecular weight phosphatase family; Region: LMWPc; cd00115 688245008647 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 688245008648 active site 688245008649 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 688245008650 dimerization interface; other site 688245008651 putative DNA binding site; other site 688245008652 putative Zn2+ binding site; other site 688245008653 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 688245008654 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 688245008655 active site 1 688245008656 dimer interface; other site 688245008657 hexamer interface; other site 688245008658 active site 2 688245008659 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 688245008660 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245008661 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 688245008662 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 688245008663 active site 688245008664 catalytic residues; other site 688245008665 metal-binding site 688245008666 DmpG-like communication domain; Region: DmpG_comm; pfam07836 688245008667 acetaldehyde dehydrogenase; Validated; Region: PRK08300 688245008668 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245008669 Prokaryotic acetaldehyde dehydrogenase, dimerization; Region: AcetDehyd-dimer; pfam09290 688245008670 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245008671 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 688245008672 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; cl12031 688245008673 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 688245008674 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 688245008675 NAD binding site; other site 688245008676 catalytic residues; other site 688245008677 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245008678 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245008679 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 688245008680 dimerization interface; other site 688245008681 putative substrate binding pocket; other site 688245008682 Domain of unknown function (DUF336); Region: DUF336; cl01249 688245008683 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 688245008684 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 688245008685 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 688245008686 tetramer interface; other site 688245008687 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 688245008688 tetramer interface; other site 688245008689 active site 688245008690 Fe binding site; other site 688245008691 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 688245008692 catalytic loop; other site 688245008693 iron binding site; other site 688245008694 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 688245008695 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 688245008696 catalytic loop; other site 688245008697 iron binding site; other site 688245008698 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...; Region: FNR_like; cl06868 688245008699 FAD binding pocket; other site 688245008700 conserved FAD binding motif; other site 688245008701 phosphate binding motif; other site 688245008702 beta-alpha-beta structure motif; other site 688245008703 NAD binding pocket; other site 688245008704 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 688245008705 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 688245008706 dimerization interface; other site 688245008707 putative path to active site cavity; other site 688245008708 diiron center; other site 688245008709 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 688245008710 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 688245008711 dimerization interface; other site 688245008712 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 688245008713 Activator of aromatic catabolism; Region: XylR_N; pfam06505 688245008714 V4R domain; Region: V4R; cl08369 688245008715 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 688245008716 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...; Region: AAA; cd00009 688245008717 Walker A motif; other site 688245008718 ATP binding site; other site 688245008719 Walker B motif; other site 688245008720 arginine finger; other site 688245008721 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245008722 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245008723 DNA binding site 688245008724 FCD domain; Region: FCD; cl11656 688245008725 Predicted membrane protein [Function unknown]; Region: COG2860 688245008726 UPF0126 domain; Region: UPF0126; pfam03458 688245008727 UPF0126 domain; Region: UPF0126; pfam03458 688245008728 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; cl12011 688245008729 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 688245008730 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008731 Domain of unknown function DUF21; Region: DUF21; pfam01595 688245008732 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 688245008733 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 688245008734 Transporter associated domain; Region: CorC_HlyC; pfam03471 688245008735 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 688245008736 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 688245008737 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 688245008738 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 688245008739 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 688245008740 Active Sites; active site 688245008741 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 688245008742 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 688245008743 Active Sites; active site 688245008744 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 688245008745 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245008746 G1 box; other site 688245008747 GTP/Mg2+ binding site; other site 688245008748 G2 box; other site 688245008749 Switch I region; other site 688245008750 G3 box; other site 688245008751 Switch II region; other site 688245008752 G4 box; other site 688245008753 G5 box; other site 688245008754 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...; Region: CysN_NodQ_II; cd03695 688245008755 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...; Region: CysN_NoDQ_III; cd04095 688245008756 Ferredoxin [Energy production and conversion]; Region: COG1146 688245008757 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 688245008758 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 688245008759 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008760 Permease family; Region: Xan_ur_permease; cl00967 688245008761 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...; Region: Pep_deformylase; cd00487 688245008762 active site 688245008763 catalytic residues; other site 688245008764 metal-binding site 688245008765 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008766 Predicted flavoproteins [General function prediction only]; Region: COG2081 688245008767 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245008768 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 688245008769 catalytic residues; other site 688245008770 transcription termination factor Rho; Provisional; Region: rho; PRK09376 688245008771 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 688245008772 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...; Region: Rho_CSD; cd04459 688245008773 RNA binding site; other site 688245008774 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...; Region: rho_factor; cd01128 688245008775 multimer interface; other site 688245008776 Walker A motif; other site 688245008777 ATP binding site; other site 688245008778 Walker B motif; other site 688245008779 NodT family; Region: outer_NodT; TIGR01845 688245008780 Outer membrane efflux protein; Region: OEP; pfam02321 688245008781 Outer membrane efflux protein; Region: OEP; pfam02321 688245008782 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 688245008783 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...; Region: Biotinyl_lipoyl_domains; cl11404 688245008784 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 688245008785 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245008786 Walker A/P-loop; other site 688245008787 ATP binding site; other site 688245008788 Q-loop/lid; other site 688245008789 ABC transporter signature motif; other site 688245008790 Walker B; other site 688245008791 D-loop; other site 688245008792 H-loop/switch region; other site 688245008793 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245008794 Walker A/P-loop; other site 688245008795 ATP binding site; other site 688245008796 Q-loop/lid; other site 688245008797 ABC transporter signature motif; other site 688245008798 Walker B; other site 688245008799 D-loop; other site 688245008800 H-loop/switch region; other site 688245008801 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 688245008802 ABC-2 type transporter; Region: ABC2_membrane; cl11417 688245008803 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 688245008804 ABC-2 type transporter; Region: ABC2_membrane; cl11417 688245008805 Acetokinase family; Region: Acetate_kinase; cl01029 688245008806 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 688245008807 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 688245008808 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 688245008809 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 688245008810 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 688245008811 putative efflux protein, MATE family; Region: matE; TIGR00797 688245008812 MatE; Region: MatE; pfam01554 688245008813 MatE; Region: MatE; pfam01554 688245008814 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 688245008815 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 688245008816 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 trans-...; Region: HisKA; cd00082 688245008817 dimer interface; other site 688245008818 phosphorylation site 688245008819 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 688245008820 ATP binding site; other site 688245008821 Mg2+ binding site; other site 688245008822 G-X-G motif; other site 688245008823 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 688245008824 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 688245008825 active site 688245008826 phosphorylation site 688245008827 intermolecular recognition site; other site 688245008828 dimerization interface; other site 688245008829 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...; Region: trans_reg_C; cd00383 688245008830 DNA binding site 688245008831 transcriptional regulator PhoU; Provisional; Region: PRK11115 688245008832 PhoU domain; Region: PhoU; pfam01895 688245008833 PhoU domain; Region: PhoU; pfam01895 688245008834 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 688245008835 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 688245008836 Walker A/P-loop; other site 688245008837 ATP binding site; other site 688245008838 Q-loop/lid; other site 688245008839 ABC transporter signature motif; other site 688245008840 Walker B; other site 688245008841 D-loop; other site 688245008842 H-loop/switch region; other site 688245008843 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...; Region: TM_PBP2; cl00427 688245008844 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...; Region: TM_PBP2; cd06261 688245008845 dimer interface; other site 688245008846 conserved gate region; other site 688245008847 putative PBP binding loops; other site 688245008848 ABC-ATPase subunit interface; other site 688245008849 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...; Region: TM_PBP2; cl00427 688245008850 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 688245008851 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 688245008852 exopolyphosphatase; Region: exo_poly_only; TIGR03706 688245008853 polyphosphate kinase; Provisional; Region: PRK05443 688245008854 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 688245008855 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 UDP-N-...; Region: GlmM; cd05802 688245008856 active site 688245008857 substrate binding site; other site 688245008858 metal-binding site 688245008859 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 688245008860 substrate binding pocket; other site 688245008861 dimer interface; other site 688245008862 inhibitor binding site; inhibition site 688245008863 FtsH Extracellular; Region: FtsH_ext; pfam06480 688245008864 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 688245008865 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...; Region: AAA; cd00009 688245008866 Walker A motif; other site 688245008867 ATP binding site; other site 688245008868 Walker B motif; other site 688245008869 arginine finger; other site 688245008870 Peptidase family M41; Region: Peptidase_M41; pfam01434 688245008871 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; cl12011 688245008872 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 688245008873 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 688245008874 Protein of unknown function (DUF2843); Region: DUF2843; pfam11004 688245008875 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 688245008876 domain; Region: GreA_GreB_N; pfam03449 688245008877 C-term; Region: GreA_GreB; pfam01272 688245008878 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 688245008879 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245008880 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245008881 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 688245008882 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245008883 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245008884 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 688245008885 IMP binding site; other site 688245008886 dimer interface; other site 688245008887 interdomain contacts; other site 688245008888 partial ornithine binding site; other site 688245008889 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 688245008890 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 688245008891 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 688245008892 catalytic site; other site 688245008893 subunit interface; other site 688245008894 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 688245008895 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 688245008896 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 688245008897 RNA/DNA hybrid binding site; other site 688245008898 active site 688245008899 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 688245008900 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 688245008901 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 688245008902 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...; Region: LbH_UDP-GlcNAc_AT; cd03351 688245008903 active site 688245008904 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 688245008905 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 688245008906 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 688245008907 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-2,3-...; Region: LbH_LpxD; cd03352 688245008908 trimer interface; other site 688245008909 active site 688245008910 UDP-GlcNAc binding site; other site 688245008911 lipid-binding site 688245008912 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 688245008913 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 688245008914 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 688245008915 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245008916 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245008917 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245008918 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245008919 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 688245008920 Surface antigen; Region: Bac_surface_Ag; cl03097 688245008921 zinc metallopeptidase RseP; Provisional; Region: PRK10779 688245008922 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 688245008923 active site 688245008924 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...; Region: PDZ_metalloprotease; cd00989 688245008925 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 688245008926 putative substrate binding region; other site 688245008927 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 688245008928 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 688245008929 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 688245008930 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 688245008931 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 688245008932 catalytic residue; other site 688245008933 putative FPP diphosphate binding site; other site 688245008934 putative FPP binding hydrophobic cleft; other site 688245008935 dimer interface; other site 688245008936 putative IPP diphosphate binding site; other site 688245008937 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 round of...; Region: RRF; cd00520 688245008938 hinge region; other site 688245008939 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 688245008940 putative nucleotide binding site; other site 688245008941 uridine monophosphate binding site; other site 688245008942 homohexameric interface; other site 688245008943 elongation factor Ts; Provisional; Region: tsf; PRK09377 688245008944 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 688245008945 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 688245008946 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 688245008947 rRNA interaction site; other site 688245008948 S8 interaction site; other site 688245008949 putative laminin-1 binding site; other site 688245008950 amidase; Provisional; Region: PRK07056 688245008951 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; cl11426 688245008952 putative carbohydrate kinase; Provisional; Region: PRK10565 688245008953 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 688245008954 putative substrate binding site; other site 688245008955 putative ATP binding site; other site 688245008956 ribonuclease R; Region: RNase_R; TIGR02063 688245008957 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 688245008958 RNB domain; Region: RNB; pfam00773 688245008959 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 play an...; Region: S1_RNase_R; cd04471 688245008960 RNA binding site; other site 688245008961 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 688245008962 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 688245008963 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 688245008964 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 688245008965 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 688245008966 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 688245008967 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 catalyze...; Region: LT_GEWL; cd00254 688245008968 N-acetyl-D-glucosamine binding site; other site 688245008969 catalytic residue; other site 688245008970 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...; Region: SHMT; cd00378 688245008971 dimer interface; other site 688245008972 glycine-pyridoxal phosphate binding site; other site 688245008973 active site 688245008974 folate binding site; other site 688245008975 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 688245008976 ATP cone domain; Region: ATP-cone; pfam03477 688245008977 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 688245008978 Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain; Region: MPP_YhcR_N; cd07412 688245008979 putative active site; other site 688245008980 putative metal binding site; other site 688245008981 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 688245008982 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 688245008983 Tetramer interface; other site 688245008984 active site 688245008985 FMN-binding site; other site 688245008986 FOG: CBS domain [General function prediction only]; Region: COG0517 688245008987 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-...; Region: CBS_pair; cl10010 688245008988 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 688245008989 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 688245008990 homodimer interface; other site 688245008991 substrate-cofactor binding pocket; other site 688245008992 pyridoxal 5'-phosphate binding site; other site 688245008993 catalytic residue; other site 688245008994 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245008995 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; cl12031 688245008996 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; cl12031 688245008997 nucleophilic elbow; other site 688245008998 catalytic triad; other site 688245008999 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 688245009000 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 688245009001 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245009002 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; cl12031 688245009003 Protein of unknown function (DUF962); Region: DUF962; cl01879 688245009004 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 688245009005 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 688245009006 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 688245009007 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245009008 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009009 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 688245009010 dimerization interface; other site 688245009011 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 688245009012 FAD binding domain; Region: FAD_binding_4; pfam01565 688245009013 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 688245009014 dimerization interface; other site 688245009015 active site 688245009016 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 5,10...; Region: DHFR; cd00209 688245009017 folate binding site; other site 688245009018 NADP+ binding site; other site 688245009019 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245009020 active site 688245009021 metal-binding site 688245009022 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245009023 Domain of unknown function (DUF333); Region: DUF333; pfam03891 688245009024 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245009025 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009026 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 688245009027 putative effector binding pocket; other site 688245009028 dimerization interface; other site 688245009029 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 688245009030 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 688245009031 Sulfatase; Region: Sulfatase; cl10460 688245009032 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...; Region: gram_neg_porins; cd00342 688245009033 trimer interface; other site 688245009034 eyelet of channel; other site 688245009035 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 688245009036 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 688245009037 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 688245009038 active site 688245009039 phosphorylation site 688245009040 intermolecular recognition site; other site 688245009041 dimerization interface; other site 688245009042 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...; Region: AAA; cd00009 688245009043 Walker A motif; other site 688245009044 ATP binding site; other site 688245009045 Walker B motif; other site 688245009046 arginine finger; other site 688245009047 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245009048 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 688245009049 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 trans...; Region: HisKA; cd00082 688245009050 dimer interface; other site 688245009051 phosphorylation site 688245009052 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 688245009053 ATP binding site; other site 688245009054 Mg2+ binding site; other site 688245009055 G-X-G motif; other site 688245009056 glutamine synthetase; Provisional; Region: glnA; PRK09469 688245009057 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 688245009058 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 688245009059 Protein of unknown function (DUF540); Region: DUF540; cl01126 688245009060 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 688245009061 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 688245009062 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...; Region: WD40; cl02567 688245009063 structural tetrad; other site 688245009064 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 688245009065 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245009066 adenylosuccinate synthetase; Provisional; Region: PRK01117 688245009067 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245009068 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245009069 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 688245009070 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 ATP-dependent...; Region: HisRS-like_core; cd00773 688245009071 dimer interface; other site 688245009072 motif 1; other site 688245009073 active site 688245009074 motif 2; other site 688245009075 motif 3; other site 688245009076 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 688245009077 FtsH protease regulator HflC; Provisional; Region: PRK11029 688245009078 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 688245009079 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 688245009080 HflK protein; Region: hflK; TIGR01933 688245009081 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 688245009082 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 688245009083 G1 box; other site 688245009084 GTP/Mg2+ binding site; other site 688245009085 Switch I region; other site 688245009086 G2 box; other site 688245009087 G3 box; other site 688245009088 Switch II region; other site 688245009089 G4 box; other site 688245009090 G5 box; other site 688245009091 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 688245009092 Sm1 motif; other site 688245009093 intra - hexamer interaction site; other site 688245009094 inter - hexamer interaction site; other site 688245009095 nucleotide binding pocket; other site 688245009096 Sm2 motif; other site 688245009097 GTP-binding protein Der; Reviewed; Region: PRK00093 688245009098 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 688245009099 G1 box; other site 688245009100 GTP/Mg2+ binding site; other site 688245009101 Switch I region; other site 688245009102 G2 box; other site 688245009103 Switch II region; other site 688245009104 G3 box; other site 688245009105 G4 box; other site 688245009106 G5 box; other site 688245009107 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 688245009108 G1 box; other site 688245009109 GTP/Mg2+ binding site; other site 688245009110 Switch I region; other site 688245009111 G2 box; other site 688245009112 G3 box; other site 688245009113 Switch II region; other site 688245009114 G4 box; other site 688245009115 G5 box; other site 688245009116 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 688245009117 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 688245009118 active site 688245009119 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 688245009120 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 688245009121 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 688245009122 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 ATP-dependent...; Region: HisRS-like_core; cd00773 688245009123 dimer interface; other site 688245009124 motif 1; other site 688245009125 active site 688245009126 motif 2; other site 688245009127 motif 3; other site 688245009128 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 688245009129 anticodon binding site; other site 688245009130 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 688245009131 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 688245009132 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 688245009133 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 688245009134 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 688245009135 binding surface 688245009136 TPR motif; other site 688245009137 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 688245009138 binding surface 688245009139 TPR motif; other site 688245009140 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 688245009141 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; cl14056 688245009142 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 688245009143 active site 688245009144 multimer interface; other site 688245009145 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 688245009146 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 688245009147 RNA binding surface; other site 688245009148 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 688245009149 probable active site; other site 688245009150 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 688245009151 ribonuclease E; Reviewed; Region: rne; PRK10811 688245009152 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 688245009153 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 688245009154 RNA binding surface; other site 688245009155 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 688245009156 active site 688245009157 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 688245009158 Peptidase family M23; Region: Peptidase_M23; pfam01551 688245009159 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; cl12011 688245009160 Survival protein SurE; Region: SurE; cl00448 688245009161 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 688245009162 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 688245009163 NAD(P) binding site; other site 688245009164 PhoD-like phosphatase; Region: PhoD; pfam09423 688245009165 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 688245009166 putative active site; other site 688245009167 putative metal binding site; other site 688245009168 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245009169 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245009170 active site 688245009171 signature motif; other site 688245009172 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 688245009173 active site 688245009174 signature motif; other site 688245009175 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 688245009176 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009177 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 688245009178 methionine aminopeptidase; Reviewed; Region: PRK07281 688245009179 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 688245009180 active site 688245009181 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 688245009182 Predicted esterase [General function prediction only]; Region: COG0400 688245009183 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; cl12031 688245009184 RF-1 domain; Region: RF-1; cl02875 688245009185 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 688245009186 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; cl12031 688245009187 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 688245009188 trimer interface; other site 688245009189 active site 688245009190 dimer interface; other site 688245009191 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 688245009192 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245009193 HIGH motif; other site 688245009194 active site 688245009195 nucleotide binding site; other site 688245009196 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245009197 KMSKS motif; other site 688245009198 active site 688245009199 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 688245009200 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 688245009201 hypothetical protein; Provisional; Region: PRK11367 688245009202 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 688245009203 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 688245009204 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 688245009205 Peptidase family M23; Region: Peptidase_M23; pfam01551 688245009206 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 688245009207 META domain; Region: META; cl01245 688245009208 enterobactin exporter EntS; Provisional; Region: PRK10489 688245009209 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 688245009210 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 688245009211 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245009212 Predicted permeases [General function prediction only]; Region: RarD; COG2962 688245009213 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 688245009214 active site 688245009215 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 688245009216 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245009217 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245009218 PAS domain S-box; Region: sensory_box; TIGR00229 688245009219 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 688245009220 putative active site; other site 688245009221 heme pocket; other site 688245009222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245009223 metal-binding site 688245009224 active site 688245009225 I-site; other site 688245009226 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 688245009227 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 688245009228 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 688245009229 GTP/Mg2+ binding site; other site 688245009230 G4 box; other site 688245009231 G5 box; other site 688245009232 G1 box; other site 688245009233 Switch I region; other site 688245009234 G2 box; other site 688245009235 G3 box; other site 688245009236 Switch II region; other site 688245009237 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 688245009238 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245009239 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245009240 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl01099 688245009241 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245009242 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 688245009243 NAD(P) binding site; other site 688245009244 active site 688245009245 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 688245009246 catalytic loop; other site 688245009247 iron binding site; other site 688245009248 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 688245009249 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 688245009250 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 688245009251 dimerization interface; other site 688245009252 active site 688245009253 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 688245009254 homopentamer interface; other site 688245009255 active site 688245009256 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 rRNA-...; Region: NusB_Sun; cl00223 688245009257 putative RNA binding site; other site 688245009258 methionine aminotransferase; Validated; Region: PRK09082 688245009259 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 688245009260 pyridoxal 5'-phosphate binding site; other site 688245009261 homodimer interface; other site 688245009262 catalytic residue; other site 688245009263 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...; Region: 4HBT; cd00586 688245009264 active site 688245009265 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 688245009266 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 688245009267 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 688245009268 Gram-negative bacterial tonB protein; Region: TonB; cl10048 688245009269 hypothetical protein; Reviewed; Region: PRK09588 688245009270 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 688245009271 RF-1 domain; Region: RF-1; cl02875 688245009272 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245009273 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009274 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 688245009275 dimerization interface; other site 688245009276 putative protease; Provisional; Region: PRK15452 688245009277 Peptidase family U32; Region: Peptidase_U32; cl03113 688245009278 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245009279 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009280 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245009281 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 688245009282 acyl-CoA synthetase; Validated; Region: PRK06188 688245009283 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245009284 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA)...; Region: CCL_ACL-C; cd06100 688245009285 active site 688245009286 oxalacetate binding site; other site 688245009287 citrylCoA binding site; other site 688245009288 coenzyme A binding site; other site 688245009289 catalytic triad; other site 688245009290 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 688245009291 classical (c) SDRs; Region: SDR_c; cd05233 688245009292 NAD(P) binding site; other site 688245009293 active site 688245009294 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 688245009295 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 688245009296 N-terminal plug; other site 688245009297 ligand-binding site; other site 688245009298 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245009299 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 688245009300 potential frameshift: common BLAST hit: gi|160897882|ref|YP_001563464.1| aconitate hydratase 688245009301 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 688245009302 ligand binding site; other site 688245009303 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 688245009304 substrate binding site; other site 688245009305 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 688245009306 substrate binding site; other site 688245009307 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245009308 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 688245009309 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245009310 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245009311 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 688245009312 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 688245009313 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245009314 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245009315 active site 688245009316 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245009317 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009318 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 688245009319 dimerization interface; other site 688245009320 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245009321 Sodium:solute symporter family; Region: SSF; cl00456 688245009322 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245009323 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245009324 DNA binding site 688245009325 FCD domain; Region: FCD; cl11656 688245009326 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 688245009327 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245009328 DNA binding site 688245009329 FCD domain; Region: FCD; cl11656 688245009330 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 688245009331 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 688245009332 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 688245009333 Ferritin-like domain; Region: Ferritin; pfam00210 688245009334 heme binding site; other site 688245009335 ferroxidase pore; other site 688245009336 ferroxidase diiron center; other site 688245009337 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 688245009338 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 688245009339 non-specific DNA binding site; other site 688245009340 salt bridge; other site 688245009341 sequence-specific DNA binding site; other site 688245009342 FCD domain; Region: FCD; cl11656 688245009343 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...; Region: gram_neg_porins; cd00342 688245009344 trimer interface; other site 688245009345 eyelet of channel; other site 688245009346 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 688245009347 extended (e) SDRs; Region: SDR_e; cd08946 688245009348 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 688245009349 NAD(P) binding site; other site 688245009350 active site 688245009351 substrate binding site; other site 688245009352 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; cl12031 688245009353 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 688245009354 homotrimer interaction site; other site 688245009355 putative active site; other site 688245009356 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 688245009357 FAD binding domain; Region: FAD_binding_4; pfam01565 688245009358 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 688245009359 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 688245009360 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...; Region: AcnB_Swivel; cd01576 688245009361 substrate binding site; other site 688245009362 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 688245009363 substrate binding site; other site 688245009364 ligand binding site; other site 688245009365 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245009366 trans-aconitate 2-methyltransferase; Provisional; Region: PRK01683 688245009367 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 688245009368 S-adenosylmethionine binding site; other site 688245009369 malate dehydrogenase; Provisional; Region: PRK05442 688245009370 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 688245009371 NAD(P) binding site; other site 688245009372 dimer interface; other site 688245009373 malate binding site; other site 688245009374 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 688245009375 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245009376 DNA binding site 688245009377 UTRA domain; Region: UTRA; cl06649 688245009378 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 688245009379 Iron-sulfur protein interface; other site 688245009380 proximal quinone binding site; other site 688245009381 SdhD (CybS) interface; other site 688245009382 proximal heme binding site; other site 688245009383 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 688245009384 SdhC subunit interface; other site 688245009385 proximal heme binding site; other site 688245009386 cardiolipin binding site; other site 688245009387 Iron-sulfur protein interface; other site 688245009388 proximal quinone binding site; other site 688245009389 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 688245009390 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009391 domain; Region: Succ_DH_flav_C; pfam02910 688245009392 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 688245009393 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 688245009394 dimer interface; other site 688245009395 Citrate synthase; Region: Citrate_synt; pfam00285 688245009396 active site 688245009397 citrylCoA binding site; other site 688245009398 NADH binding; other site 688245009399 cationic pore residues; other site 688245009400 oxalacetate/citrate binding site; other site 688245009401 coenzyme A binding site; other site 688245009402 catalytic triad; other site 688245009403 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 688245009404 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 688245009405 NADP binding site; other site 688245009406 dimer interface; other site 688245009407 helicase 45; Provisional; Region: PTZ00424 688245009408 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 688245009409 ATP binding site; other site 688245009410 Mg++ binding site; other site 688245009411 motif III; other site 688245009412 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 688245009413 nucleotide binding region; other site 688245009414 ATP-binding site; other site 688245009415 DNA helicase, putative; Region: TIGR00376 688245009416 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009417 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 688245009418 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 688245009419 putative active site; other site 688245009420 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 688245009421 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 688245009422 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 688245009423 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 688245009424 conserved cys residue; other site 688245009425 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245009426 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245009427 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 688245009428 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 688245009429 substrate binding site; other site 688245009430 catalytic Zn binding site; other site 688245009431 NAD binding site; other site 688245009432 structural Zn binding site; other site 688245009433 dimer interface; other site 688245009434 Predicted esterase [General function prediction only]; Region: COG0627 688245009435 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; cl12031 688245009436 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 688245009437 Cupin domain; Region: Cupin_2; cl09118 688245009438 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 688245009439 phenol 2-monooxygenase; Provisional; Region: PRK08294 688245009440 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009441 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009442 FAD-dependent Phenol hydoxylase (PHOX) family, C-terminal TRX-fold domain; composed of proteins similar to PHOX from the aerobic topsoil yeast Trichosporon cutaneum. PHOX is a flavoprotein monooxygenase that catalyzes the hydroxylation of phenol and...; Region: PHOX_C; cd02979 688245009443 dimer interface; other site 688245009444 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245009445 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009446 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 688245009447 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 688245009448 motif II; other site 688245009449 phosphonate metabolism-associated iron-containing alcohol dehydrogenase; Region: Phn_Fe-ADH; TIGR03405 688245009450 Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP); Region: HEPD; cd08182 688245009451 putative active site; other site 688245009452 metal-binding site 688245009453 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...; Region: TM_PBP2; cd06261 688245009454 dimer interface; other site 688245009455 conserved gate region; other site 688245009456 putative PBP binding loops; other site 688245009457 ABC-ATPase subunit interface; other site 688245009458 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 688245009459 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 688245009460 Walker A/P-loop; other site 688245009461 ATP binding site; other site 688245009462 Q-loop/lid; other site 688245009463 ABC transporter signature motif; other site 688245009464 Walker B; other site 688245009465 D-loop; other site 688245009466 H-loop/switch region; other site 688245009467 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 688245009468 phosphonate ABC transporter, periplasmic phosphonate binding protein; Region: PhnD; TIGR03431 688245009469 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 688245009470 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009471 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 688245009472 dimerization interface; other site 688245009473 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 688245009474 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 688245009475 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 688245009476 FeS/SAM binding site; other site 688245009477 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 688245009478 C-term; Region: GreA_GreB; pfam01272 688245009479 Predicted acyltransferases [Lipid metabolism]; Region: COG1835; cl00792 688245009480 Acyltransferase family; Region: Acyl_transf_3; pfam01757 688245009481 Predicted transcriptional regulators [Transcription]; Region: COG1510 688245009482 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 688245009483 dimerization interface; other site 688245009484 putative DNA binding site; other site 688245009485 putative Zn2+ binding site; other site 688245009486 Transcriptional regulators [Transcription]; Region: PurR; COG1609 688245009487 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 688245009488 DNA binding site 688245009489 domain linker motif; other site 688245009490 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 688245009491 putative ligand binding site; other site 688245009492 putative dimerization interface; other site 688245009493 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 688245009494 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 688245009495 ATP-binding site; other site 688245009496 Gluconate-6-phosphate binding site; other site 688245009497 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245009498 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; cl09110 688245009499 DctM-like transporters; Region: DctM; pfam06808 688245009500 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245009501 Dehydratase family; Region: ILVD_EDD; cl00340 688245009502 6-phosphogluconate dehydratase; Region: edd; TIGR01196 688245009503 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 688245009504 KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best...; Region: KDPG_aldolase; cd00452 688245009505 active site 688245009506 intersubunit interface; other site 688245009507 catalytic residue; other site 688245009508 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 688245009509 cytochrome bd-II oxidase subunit 2; Provisional; Region: PRK15028; cl12219 688245009510 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 688245009511 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 688245009512 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 688245009513 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009514 Walker A/P-loop; other site 688245009515 ATP binding site; other site 688245009516 Q-loop/lid; other site 688245009517 ABC transporter signature motif; other site 688245009518 Walker B; other site 688245009519 D-loop; other site 688245009520 H-loop/switch region; other site 688245009521 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 688245009522 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245009523 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with...; Region: ABCC_MRP_Like; cd03228 688245009524 Walker A/P-loop; other site 688245009525 ATP binding site; other site 688245009526 Q-loop/lid; other site 688245009527 ABC transporter signature motif; other site 688245009528 Walker B; other site 688245009529 D-loop; other site 688245009530 H-loop/switch region; other site 688245009531 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 688245009532 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...; Region: NPD_like; cd04730 688245009533 FMN binding site; other site 688245009534 substrate binding site; other site 688245009535 putative catalytic residue; other site 688245009536 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245009537 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 688245009538 putative ligand binding site; other site 688245009539 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 688245009540 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 688245009541 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 688245009542 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 688245009543 Ligand binding site; other site 688245009544 enoyl-CoA hydratase; Validated; Region: PRK08139 688245009545 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 688245009546 substrate binding site; other site 688245009547 oxyanion hole (OAH) forming residues; other site 688245009548 trimer interface; other site 688245009549 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 688245009550 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 688245009551 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...; Region: AAA; cd00009 688245009552 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 688245009553 Walker A motif; other site 688245009554 ATP binding site; other site 688245009555 Walker B motif; other site 688245009556 arginine finger; other site 688245009557 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009558 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 688245009559 Protein of unknown function DUF58; Region: DUF58; pfam01882 688245009560 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 688245009561 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 688245009562 lytic murein transglycosylase; Region: MltB_2; TIGR02283 688245009563 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 catalyze...; Region: LT_GEWL; cd00254 688245009564 N-acetyl-D-glucosamine binding site; other site 688245009565 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245009566 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 688245009567 putative ligand binding site; other site 688245009568 This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa...; Region: ACD_sHsps_p23-like; cd00298 688245009569 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 688245009570 UGMP family protein; Validated; Region: PRK09604 688245009571 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 688245009572 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-...; Region: CBS_pair_10; cd04623 688245009573 FOG: CBS domain [General function prediction only]; Region: COG0517 688245009574 Uncharacterized conserved protein (DUF2302); Region: DUF2302; cl02237 688245009575 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...; Region: gram_neg_porins; cd00342 688245009576 eyelet of channel; other site 688245009577 trimer interface; other site 688245009578 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 688245009579 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 688245009580 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 688245009581 NAD(P) binding site; other site 688245009582 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 688245009583 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009584 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 688245009585 dimerization interface; other site 688245009586 substrate binding pocket; other site 688245009587 glycosyl transferase family protein; Provisional; Region: PRK08136 688245009588 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 688245009589 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245009590 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...; Region: BFIT_BACH; cd03442 688245009591 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009592 flavoprotein, HI0933 family; Region: TIGR00275 688245009593 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 688245009594 putative ligand binding site; other site 688245009595 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 688245009596 GatB domain; Region: GatB_Yqey; cl11497 688245009597 transcriptional activator TtdR; Provisional; Region: PRK09801 688245009598 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009599 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_9; cd08479 688245009600 putative effector binding pocket; other site 688245009601 putative dimerization interface; other site 688245009602 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 688245009603 Domain of unknown function (DU1801); Region: DUF1801; cl01838 688245009604 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 688245009605 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009606 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 688245009607 dimerization interface; other site 688245009608 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 688245009609 galactarate dehydratase; Region: galactar-dH20; TIGR03248 688245009610 SAF domain; Region: SAF; cl00555 688245009611 SAF domain; Region: SAF; cl00555 688245009612 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 688245009613 tetramerization interface; other site 688245009614 NAD(P) binding site; other site 688245009615 catalytic residues; other site 688245009616 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 688245009617 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245009618 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 688245009619 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 688245009620 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 688245009621 putative active site; other site 688245009622 heme pocket; other site 688245009623 GAF domain; Region: GAF; cl00853 688245009624 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245009625 metal-binding site 688245009626 active site 688245009627 I-site; other site 688245009628 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 688245009629 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 688245009630 EamA-like transporter family; Region: EamA; cl01037 688245009631 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 688245009632 Protein of unknown function (DUF615); Region: DUF615; cl01147 688245009633 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 688245009634 MPT binding site; other site 688245009635 trimer interface; other site 688245009636 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245009637 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 688245009638 putative ligand binding site; other site 688245009639 ThiC family; Region: ThiC; cl08031 688245009640 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a...; Region: Nitroreductase; cd02136 688245009641 putative FMN binding site; other site 688245009642 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245009643 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 688245009644 putative ligand binding site; other site 688245009645 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a...; Region: Nitroreductase; cd02136 688245009646 putative FMN binding site; other site 688245009647 serine O-acetyltransferase; Region: cysE; TIGR01172 688245009648 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 L...; Region: LbH_SAT; cd03354 688245009649 trimer interface; other site 688245009650 active site 688245009651 substrate binding site; other site 688245009652 CoA binding site; other site 688245009653 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 688245009654 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 688245009655 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 688245009656 dimerization interface; other site 688245009657 active site 688245009658 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 688245009659 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 688245009660 MutS domain I; Region: MutS_I; pfam01624 688245009661 MutS domain II; Region: MutS_II; pfam05188 688245009662 MutS domain III; Region: MutS_III; cl04977 688245009663 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009664 Walker A/P-loop; other site 688245009665 ATP binding site; other site 688245009666 Q-loop/lid; other site 688245009667 ABC transporter signature motif; other site 688245009668 Walker B; other site 688245009669 D-loop; other site 688245009670 H-loop/switch region; other site 688245009671 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245009672 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245009673 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245009674 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 688245009675 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...; Region: proteasome_beta_bacterial; cd03765 688245009676 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 688245009677 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; cl12031 688245009678 Bacitracin resistance protein BacA; Region: BacA; cl00858 688245009679 psiF repeat; Region: PsiF_repeat; pfam07769 688245009680 psiF repeat; Region: PsiF_repeat; pfam07769 688245009681 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245009682 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245009683 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 688245009684 N-terminal plug; other site 688245009685 ligand-binding site; other site 688245009686 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 688245009687 Histidine kinase; Region: His_kinase; pfam06580 688245009688 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 688245009689 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 688245009690 active site 688245009691 phosphorylation site 688245009692 intermolecular recognition site; other site 688245009693 dimerization interface; other site 688245009694 LytTr DNA-binding domain; Region: LytTR; cl04498 688245009695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009696 Walker A/P-loop; other site 688245009697 ATP binding site; other site 688245009698 Q-loop/lid; other site 688245009699 ABC transporter signature motif; other site 688245009700 Walker B; other site 688245009701 D-loop; other site 688245009702 H-loop/switch region; other site 688245009703 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 688245009704 putative hydrophobic ligand binding site; other site 688245009705 NodT family; Region: outer_NodT; TIGR01845 688245009706 Outer membrane efflux protein; Region: OEP; pfam02321 688245009707 Outer membrane efflux protein; Region: OEP; pfam02321 688245009708 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 688245009709 Protein export membrane protein; Region: SecD_SecF; cl14618 688245009710 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 688245009711 Protein export membrane protein; Region: SecD_SecF; cl14618 688245009712 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 688245009713 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 688245009714 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 688245009715 putative hydrophobic ligand binding site; other site 688245009716 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 688245009717 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 688245009718 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 688245009719 metal ion-dependent adhesion site (MIDAS); other site 688245009720 MoxR-like ATPases [General function prediction only]; Region: COG0714 688245009721 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 688245009722 carbon-monoxide dehydrogenase, large subunit; Region: CO_dehy_Mo_lg; TIGR02416 688245009723 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 688245009724 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245009725 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245009726 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 688245009727 catalytic loop; other site 688245009728 iron binding site; other site 688245009729 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245009730 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 688245009731 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 688245009732 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245009733 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245009734 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; cl09110 688245009735 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; cl09110 688245009736 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245009737 potential frameshift: common BLAST hit: gi|89901645|ref|YP_524116.1| twin-arginine translocation pathway signal 688245009738 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245009739 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245009740 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 688245009741 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 with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 688245009742 TPP-binding site; other site 688245009743 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 688245009744 PYR/PP interface; other site 688245009745 dimer interface; other site 688245009746 TPP binding site; other site 688245009747 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 688245009748 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 688245009749 substrate binding pocket; other site 688245009750 chain length determination region; other site 688245009751 substrate-Mg2+ binding site; other site 688245009752 catalytic residues; other site 688245009753 aspartate-rich region 1; other site 688245009754 active site lid residues 688245009755 aspartate-rich region 2; other site 688245009756 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 688245009757 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 688245009758 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 688245009759 [2Fe-2S] cluster binding site; other site 688245009760 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 688245009761 alpha subunit interface; other site 688245009762 active site 688245009763 substrate binding site; other site 688245009764 Fe binding site; other site 688245009765 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 688245009766 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...; Region: TST_Repeat_1; cd01448 688245009767 active site residue 688245009768 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 688245009769 active site residue 688245009770 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 688245009771 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 688245009772 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 688245009773 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 688245009774 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 688245009775 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 688245009776 domain interfaces; other site 688245009777 active site 688245009778 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 688245009779 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...; Region: HemD; cd06578 688245009780 active site 688245009781 HemX; Region: HemX; cl14667 688245009782 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 688245009783 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 688245009784 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245009785 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245009786 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245009787 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245009788 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 688245009789 YceI-like domain; Region: YceI; cl01001 688245009790 YceI-like domain; Region: YceI; cl01001 688245009791 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 688245009792 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 688245009793 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 688245009794 HIGH motif; other site 688245009795 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 688245009796 active site 688245009797 KMSKS motif; other site 688245009798 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 688245009799 tRNA binding surface; other site 688245009800 anticodon binding site; other site 688245009801 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 688245009802 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 688245009803 active site 688245009804 tetramer interface; other site 688245009805 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 two...; Region: SirA_YedF_YeeD; cd00291 688245009806 CPxP motif; other site 688245009807 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 688245009808 putative NADH binding site; other site 688245009809 putative active site; other site 688245009810 nudix motif; other site 688245009811 putative metal binding site; other site 688245009812 cysteine synthases; Region: cysKM; TIGR01136 688245009813 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 688245009814 dimer interface; other site 688245009815 pyridoxal 5'-phosphate binding site; other site 688245009816 catalytic residue; other site 688245009817 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...; Region: S24_LexA-like; cd06529 688245009818 Catalytic site; other site 688245009819 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 688245009820 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 688245009821 active site 688245009822 DNA binding site 688245009823 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 688245009824 catalytic residues; other site 688245009825 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 688245009826 NlpC/P60 family; Region: NLPC_P60; cl11438 688245009827 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 688245009828 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 688245009829 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 688245009830 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 688245009831 Phage-related minor tail protein [Function unknown]; Region: COG5281 688245009832 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 688245009833 phage tail tape measure protein, lambda family; Region: tape_meas_lam_C; TIGR01541 688245009834 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 688245009835 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 688245009836 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; cl00287 688245009837 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 688245009838 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 688245009839 oligomer interface; other site 688245009840 active site residues 688245009841 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 688245009842 Protein of unknown function (DUF2610); Region: DUF2610; pfam11020 688245009843 Mor transcription activator family; Region: Mor; cl02360 688245009844 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 688245009845 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 688245009846 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 688245009847 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 688245009848 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 688245009849 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 688245009850 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 688245009851 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88)...; Region: Peptidase_S24_S26; cd06462 688245009852 Catalytic site; other site 688245009853 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 688245009854 Core-2/I-Branching enzyme; Region: Branch; pfam02485 688245009855 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009856 active site 688245009857 restriction alleviation and modification protein; Reviewed; Region: lar; cl08047 688245009858 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 688245009859 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 688245009860 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl01450 688245009861 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245009862 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 688245009863 active site 688245009864 phosphorylation site 688245009865 intermolecular recognition site; other site 688245009866 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...; Region: LuxR_C_like; cd06170 688245009867 DNA binding residues 688245009868 dimerization interface; other site 688245009869 LrgA family; Region: LrgA; cl00608 688245009870 LrgB-like family; Region: LrgB; cl00596 688245009871 EamA-like transporter family; Region: EamA; cl01037 688245009872 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245009873 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009874 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 688245009875 putative effector binding pocket; other site 688245009876 dimerization interface; other site 688245009877 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl00527 688245009878 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245009879 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009880 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 688245009881 dimerization interface; other site 688245009882 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 688245009883 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 688245009884 FAD binding site; other site 688245009885 substrate binding pocket; other site 688245009886 catalytic base; other site 688245009887 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245009888 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 688245009889 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...; Region: gram_neg_porins; cd00342 688245009890 eyelet of channel; other site 688245009891 trimer interface; other site 688245009892 putative arabinose transporter; Provisional; Region: PRK03545 688245009893 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 688245009894 putative substrate translocation pore; other site 688245009895 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 688245009896 NAD binding site; other site 688245009897 substrate binding site; other site 688245009898 putative active site; other site 688245009899 transcriptional regulator; Provisional; Region: PRK10632 688245009900 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245009901 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 688245009902 putative effector binding pocket; other site 688245009903 dimerization interface; other site 688245009904 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245009905 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 688245009906 dimerization interface; other site 688245009907 ligand binding site; other site 688245009908 lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway; Region: Lumazine_synthase-like; cl00317 688245009909 active site 688245009910 homopentamer interface; other site 688245009911 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 688245009912 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 688245009913 putative NAD(P) binding site; other site 688245009914 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 688245009915 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 688245009916 catalytic loop; other site 688245009917 iron binding site; other site 688245009918 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...; Region: flavin_oxioreductase; cd06189 688245009919 FAD binding pocket; other site 688245009920 FAD binding motif; other site 688245009921 phosphate binding motif; other site 688245009922 beta-alpha-beta structure motif; other site 688245009923 NAD binding pocket; other site 688245009924 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 688245009925 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 688245009926 catalytic center binding site; other site 688245009927 ATP binding site; other site 688245009928 poly(A) polymerase; Region: pcnB; TIGR01942 688245009929 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 688245009930 active site 688245009931 NTP binding site; other site 688245009932 metal binding triad; metal-binding site 688245009933 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; cl11391 688245009934 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245009935 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 688245009936 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine...; Region: PurM; cd02196 688245009937 dimerization interface; other site 688245009938 putative ATP binding site; other site 688245009939 Domain of unknown function DUF20; Region: UPF0118; cl00465 688245009940 hypothetical protein; Provisional; Region: PRK10941 688245009941 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 688245009942 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 688245009943 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245009944 Predicted dehydrogenase [General function prediction only]; Region: COG0579 688245009945 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 688245009946 MatE; Region: MatE; pfam01554 688245009947 MatE; Region: MatE; pfam01554 688245009948 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 688245009949 acetylornithine aminotransferase; Provisional; Region: PRK02627 688245009950 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 688245009951 inhibitor-cofactor binding pocket; inhibition site 688245009952 pyridoxal 5'-phosphate binding site; other site 688245009953 catalytic residue; other site 688245009954 ornithine carbamoyltransferase; Provisional; Region: PRK00779 688245009955 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 688245009956 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 688245009957 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 688245009958 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 688245009959 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 688245009960 G1 box; other site 688245009961 GTP/Mg2+ binding site; other site 688245009962 Switch I region; other site 688245009963 G2 box; other site 688245009964 G3 box; other site 688245009965 Switch II region; other site 688245009966 G4 box; other site 688245009967 G5 box; other site 688245009968 Nucleoside recognition; Region: Gate; cl00486 688245009969 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 688245009970 Nucleoside recognition; Region: Gate; cl00486 688245009971 FeoA domain; Region: FeoA; cl00838 688245009972 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 688245009973 Protein phosphatase 2C; Region: PP2C; pfam00481 688245009974 active site 688245009975 LysE type translocator; Region: LysE; cl00565 688245009976 Cupin domain; Region: Cupin_2; cl09118 688245009977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 688245009978 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245009979 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245009980 ethanolamine permease; Region: 2A0305; TIGR00908 688245009981 Putative cyclase; Region: Cyclase; cl00814 688245009982 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 688245009983 kynureninase; Region: kynureninase; TIGR01814 688245009984 L-lactate permease; Region: Lactate_perm; cl00701 688245009985 L-lactate permease; Region: Lactate_perm; cl00701 688245009986 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 688245009987 non-specific DNA binding site; other site 688245009988 salt bridge; other site 688245009989 sequence-specific DNA binding site; other site 688245009990 Cupin domain; Region: Cupin_2; cl09118 688245009991 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 688245009992 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 688245009993 helix-hairpin-helix signature motif; other site 688245009994 substrate binding pocket; other site 688245009995 active site 688245009996 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 688245009997 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 688245009998 DNA binding site 688245009999 active site 688245010000 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 688245010001 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 688245010002 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245010003 putative substrate translocation pore; other site 688245010004 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 688245010005 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010006 H-NS histone family; Region: Histone_HNS; pfam00816 688245010007 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 688245010008 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 688245010009 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 688245010010 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 688245010011 active site 688245010012 metal-binding site 688245010013 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 688245010014 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 688245010015 ATP binding site; other site 688245010016 Mg++ binding site; other site 688245010017 motif III; other site 688245010018 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 688245010019 nucleotide binding region; other site 688245010020 ATP-binding site; other site 688245010021 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 688245010022 ornithine cyclodeaminase; Validated; Region: PRK07340 688245010023 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 688245010024 NAD(P) binding site; other site 688245010025 Quinolinate synthetase A protein; Region: NadA; cl00420 688245010026 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010027 domain; Region: Succ_DH_flav_C; pfam02910 688245010028 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 688245010029 trimer interface; other site 688245010030 active site 688245010031 guanine deaminase; Provisional; Region: PRK09228 688245010032 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 688245010033 active site 688245010034 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245010035 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 688245010036 dimerization interface; other site 688245010037 substrate binding pocket; other site 688245010038 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245010039 substrate binding pocket; other site 688245010040 active site 688245010041 iron coordination sites; other site 688245010042 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 688245010043 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; cl09108 688245010044 phosphate binding site; other site 688245010045 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life...; Region: HINT_subgroup; cd01277 688245010046 HIT family signature motif; other site 688245010047 catalytic residue; other site 688245010048 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 688245010049 active site 688245010050 purine riboside binding site; other site 688245010051 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 688245010052 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 688245010053 [2Fe-2S] cluster binding site; other site 688245010054 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 688245010055 hydrophobic ligand binding site; other site 688245010056 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 688245010057 putative ligand binding site; other site 688245010058 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 688245010059 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 688245010060 putative ligand binding site; other site 688245010061 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 688245010062 TM-ABC transporter signature motif; other site 688245010063 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 688245010064 TM-ABC transporter signature motif; other site 688245010065 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 688245010066 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 688245010067 Walker A/P-loop; other site 688245010068 ATP binding site; other site 688245010069 Q-loop/lid; other site 688245010070 ABC transporter signature motif; other site 688245010071 Walker B; other site 688245010072 D-loop; other site 688245010073 H-loop/switch region; other site 688245010074 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_II; cd03215 688245010075 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245010076 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010077 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 688245010078 dimerization interface; other site 688245010079 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 688245010080 putative active site; other site 688245010081 heme pocket; other site 688245010082 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010083 metal-binding site 688245010084 active site 688245010085 I-site; other site 688245010086 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; cl00047 688245010087 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010088 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245010089 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 688245010090 N-terminal plug; other site 688245010091 ligand-binding site; other site 688245010092 fec operon regulator FecR; Reviewed; Region: PRK09774 688245010093 FecR protein; Region: FecR; pfam04773 688245010094 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 688245010095 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245010096 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...; Region: Sigma70_r4; cl01055 688245010097 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245010098 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 688245010099 N-terminal plug; other site 688245010100 ligand-binding site; other site 688245010101 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 688245010102 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 688245010103 putative ligand binding residues; other site 688245010104 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 688245010105 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 688245010106 Walker A/P-loop; other site 688245010107 ATP binding site; other site 688245010108 Q-loop/lid; other site 688245010109 ABC transporter signature motif; other site 688245010110 Walker B; other site 688245010111 D-loop; other site 688245010112 H-loop/switch region; other site 688245010113 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...; Region: TM_ABC_iron-siderophores_like; cl00462 688245010114 ABC-ATPase subunit interface; other site 688245010115 dimer interface; other site 688245010116 putative PBP binding regions; other site 688245010117 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...; Region: TM_ABC_iron-siderophores_like; cd06550 688245010118 ABC-ATPase subunit interface; other site 688245010119 dimer interface; other site 688245010120 putative PBP binding regions; other site 688245010121 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 688245010122 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245010123 Walker A/P-loop; other site 688245010124 ATP binding site; other site 688245010125 Q-loop/lid; other site 688245010126 ABC transporter signature motif; other site 688245010127 Walker B; other site 688245010128 D-loop; other site 688245010129 H-loop/switch region; other site 688245010130 potential frameshift: common BLAST hit: gi|26989315|ref|NP_744740.1| ABC transporter, permease/ATP-binding protein, putative 688245010131 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245010132 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 688245010133 Walker A/P-loop; other site 688245010134 ATP binding site; other site 688245010135 Q-loop/lid; other site 688245010136 ABC transporter signature motif; other site 688245010137 Walker B; other site 688245010138 D-loop; other site 688245010139 H-loop/switch region; other site 688245010140 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 688245010141 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245010142 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 688245010143 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245010144 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245010145 Protein of unknown function (DUF989); Region: DUF989; pfam06181 688245010146 Cytochrome c; Region: Cytochrom_C; cl11414 688245010147 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 688245010148 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 688245010149 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010150 Family of unknown function (DUF500); Region: DUF500; cl01109 688245010151 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 688245010152 active site 688245010153 homotetramer interface; other site 688245010154 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 688245010155 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 688245010156 tartronate semialdehyde reductase; Provisional; Region: PRK15059 688245010157 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 688245010158 glyoxylate carboligase; Provisional; Region: PRK11269 688245010159 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 688245010160 PYR/PP interface; other site 688245010161 dimer interface; other site 688245010162 TPP binding site; other site 688245010163 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 688245010164 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...; Region: TPP_enzymes; cl01629 688245010165 TPP-binding site; other site 688245010166 transcriptional regulator; Provisional; Region: PRK10632 688245010167 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010168 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 688245010169 putative effector binding pocket; other site 688245010170 dimerization interface; other site 688245010171 MOFRL family; Region: MOFRL; cl01013 688245010172 potential frameshift: common BLAST hit: gi|160897554|ref|YP_001563136.1| GntR family transcriptional regulator 688245010173 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245010174 DNA binding site 688245010175 FCD domain; Region: FCD; cl11656 688245010176 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 688245010177 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 688245010178 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional; Region: PRK13590 688245010179 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 688245010180 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245010181 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245010182 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245010183 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 688245010184 transcriptional regulator; Provisional; Region: PRK10632 688245010185 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010186 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 688245010187 dimerization interface; other site 688245010188 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 688245010189 putative substrate translocation pore; other site 688245010190 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245010191 Permease family; Region: Xan_ur_permease; cl00967 688245010192 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 688245010193 Malic enzyme, N-terminal domain; Region: malic; pfam00390 688245010194 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 688245010195 putative NAD(P) binding site; other site 688245010196 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 688245010197 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 688245010198 Sel1 repeat; Region: Sel1; cl02723 688245010199 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 688245010200 non-specific DNA binding site; other site 688245010201 salt bridge; other site 688245010202 sequence-specific DNA binding site; other site 688245010203 IS2 transposase TnpB; Reviewed; Region: PRK09409 688245010204 DNA sulfur modification protein DndD; Region: DNA_S_dndD; TIGR03185 688245010205 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 688245010206 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...; Region: AAA; cd00009 688245010207 Walker A motif; other site 688245010208 ATP binding site; other site 688245010209 Walker B motif; other site 688245010210 arginine finger; other site 688245010211 DoxX; Region: DoxX; cl00976 688245010212 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245010213 EamA-like transporter family; Region: EamA; cl01037 688245010214 Pirin-related protein [General function prediction only]; Region: COG1741 688245010215 Cupin domain; Region: Cupin_2; cl09118 688245010216 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 688245010217 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245010218 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010219 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 688245010220 putative effector binding pocket; other site 688245010221 putative dimerization interface; other site 688245010222 NodT family; Region: outer_NodT; TIGR01845 688245010223 Outer membrane efflux protein; Region: OEP; pfam02321 688245010224 Outer membrane efflux protein; Region: OEP; pfam02321 688245010225 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 688245010226 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 688245010227 Walker A/P-loop; other site 688245010228 ATP binding site; other site 688245010229 Q-loop/lid; other site 688245010230 ABC transporter signature motif; other site 688245010231 Walker B; other site 688245010232 D-loop; other site 688245010233 H-loop/switch region; other site 688245010234 Predicted permease; Region: FtsX; cl11418 688245010235 macrolide transporter subunit MacA; Provisional; Region: PRK11578 688245010236 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 688245010237 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 688245010238 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 688245010239 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 688245010240 N-terminal plug; other site 688245010241 ligand-binding site; other site 688245010242 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 688245010243 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 688245010244 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010245 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 688245010246 intersubunit interface; other site 688245010247 active site 688245010248 Zn2+ binding site; other site 688245010249 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 688245010250 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245010251 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 688245010252 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 688245010253 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 688245010254 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 688245010255 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 688245010256 Ligand binding site; other site 688245010257 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 688245010258 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...; Region: NPD_like; cd04730 688245010259 FMN binding site; other site 688245010260 substrate binding site; other site 688245010261 putative catalytic residue; other site 688245010262 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 688245010263 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 688245010264 CoA-transferase family III; Region: CoA_transf_3; cl00778 688245010265 enoyl-CoA hydratase; Provisional; Region: PRK07511 688245010266 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 688245010267 substrate binding site; other site 688245010268 oxyanion hole (OAH) forming residues; other site 688245010269 trimer interface; other site 688245010270 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 688245010271 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 688245010272 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 688245010273 active site 688245010274 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 688245010275 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245010276 active site 688245010277 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 688245010278 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 688245010279 dimer interface; other site 688245010280 active site 688245010281 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 688245010282 substrate binding site; other site 688245010283 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 688245010284 oxyanion hole (OAH) forming residues; other site 688245010285 trimer interface; other site 688245010286 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010287 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245010288 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245010289 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245010290 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010291 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 688245010292 putative effector binding pocket; other site 688245010293 dimerization interface; other site 688245010294 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245010295 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245010296 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 688245010297 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245010298 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 688245010299 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 688245010300 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 688245010301 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 688245010302 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 688245010303 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245010304 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245010305 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 688245010306 potential frameshift: common BLAST hit: gi|160899363|ref|YP_001564945.1| gluconate 2-dehydrogenase (acceptor) 688245010307 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 688245010308 Cytochrome c; Region: Cytochrom_C; cl11414 688245010309 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 688245010310 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 688245010311 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 688245010312 aspartate racemase; Region: asp_race; TIGR00035 688245010313 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245010314 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 688245010315 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 688245010316 active site 688245010317 substrate binding site; other site 688245010318 Mg2+ binding site; other site 688245010319 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 688245010320 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245010321 DNA binding site 688245010322 UTRA domain; Region: UTRA; cl06649 688245010323 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010324 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 688245010325 NAD(P) binding site; other site 688245010326 active site 688245010327 fumarylacetoacetase; Region: PLN02856 688245010328 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 688245010329 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245010330 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 688245010331 Sporulation related domain; Region: SPOR; cl10051 688245010332 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 688245010333 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 688245010334 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 688245010335 FeS/SAM binding site; other site 688245010336 HemN C-terminal region; Region: HemN_C; pfam06969 688245010337 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 Ham1-...; Region: HAM1; cd00515 688245010338 active site 688245010339 dimerization interface; other site 688245010340 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 688245010341 Protein phosphatase 2C; Region: PP2C; pfam00481 688245010342 active site 688245010343 Protein kinase domain; Region: Pkinase; pfam00069 688245010344 Catalytic domain of Protein Kinases; Region: PKc; cd00180 688245010345 active site 688245010346 ATP binding site; other site 688245010347 substrate binding site; other site 688245010348 activation loop (A-loop); other site 688245010349 hypothetical protein; Provisional; Region: PRK11820 688245010350 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 688245010351 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 688245010352 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...; Region: GMPK; cd00071 688245010353 catalytic site; other site 688245010354 G-X2-G-X-G-K; other site 688245010355 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 688245010356 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 688245010357 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245010358 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 688245010359 synthetase active site; other site 688245010360 NTP binding site; other site 688245010361 metal-binding site 688245010362 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...; Region: TGS_RelA_SpoT; cd01668 688245010363 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 688245010364 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 688245010365 lytic murein transglycosylase; Region: MltB_2; TIGR02283 688245010366 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 688245010367 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 688245010368 domain; Region: GreA_GreB_N; pfam03449 688245010369 C-term; Region: GreA_GreB; pfam01272 688245010370 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245010371 DNA binding site 688245010372 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 688245010373 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 688245010374 pyridoxal 5'-phosphate binding site; other site 688245010375 homodimer interface; other site 688245010376 catalytic residue; other site 688245010377 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245010378 Amino acid permease; Region: AA_permease; pfam00324 688245010379 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 688245010380 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010381 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 688245010382 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010383 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 688245010384 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...; Region: PBPb; cd00134 688245010385 substrate binding pocket; other site 688245010386 membrane-bound complex binding site; other site 688245010387 hinge residues; other site 688245010388 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 688245010389 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245010390 Walker A/P-loop; other site 688245010391 ATP binding site; other site 688245010392 Q-loop/lid; other site 688245010393 ABC transporter signature motif; other site 688245010394 Walker B; other site 688245010395 D-loop; other site 688245010396 H-loop/switch region; other site 688245010397 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...; Region: TM_PBP2; cd06261 688245010398 dimer interface; other site 688245010399 conserved gate region; other site 688245010400 putative PBP binding loops; other site 688245010401 ABC-ATPase subunit interface; other site 688245010402 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 688245010403 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 688245010404 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 688245010405 metal ion-dependent adhesion site (MIDAS); other site 688245010406 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 688245010407 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 688245010408 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245010409 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010410 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245010411 sulfoacetaldehyde acetyltransferase; Validated; Region: PRK07525 688245010412 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 688245010413 PYR/PP interface; other site 688245010414 dimer interface; other site 688245010415 TPP binding site; other site 688245010416 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 688245010417 TPP-binding module; composed of proteins similar to Alcaligenes defragrans sulfoacetaldehyde acetyltransferase (Xsc). Xsc plays a key role in the degradation of taurine, catalyzing the desulfonation of 2-sulfoacetaldehyde into sulfite and acetyl...; Region: TPP_Xsc_like; cd02013 688245010418 TPP-binding site; other site 688245010419 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 688245010420 IS2 transposase TnpB; Reviewed; Region: PRK09409 688245010421 Integrase core domain; Region: rve; cl01316 688245010422 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; cl01116 688245010423 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 688245010424 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 688245010425 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 688245010426 catalytic residues; other site 688245010427 catalytic nucleophile; other site 688245010428 Presynaptic Site I dimer interface; other site 688245010429 Synaptic Antiparallel dimer interface; other site 688245010430 Synaptic Flat tetramer interface; other site 688245010431 Synaptic Site I dimer interface; other site 688245010432 DNA binding site 688245010433 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 688245010434 Int/Topo IB signature motif; other site 688245010435 active site 688245010436 DNA binding site 688245010437 seryl-tRNA synthetase; Provisional; Region: PRK05431 688245010438 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 688245010439 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 688245010440 dimer interface; other site 688245010441 active site 688245010442 motif 1; other site 688245010443 motif 2; other site 688245010444 motif 3; other site 688245010445 LytB protein; Region: LYTB; cl00507 688245010446 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 688245010447 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245010448 hypothetical protein; Reviewed; Region: PRK00024 688245010449 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 688245010450 MPN+ (JAMM) motif; other site 688245010451 Zinc-binding site; other site 688245010452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 688245010453 Smr domain; Region: Smr; cl02619 688245010454 Peptidase family M48; Region: Peptidase_M48; cl12018 688245010455 LemA family; Region: LemA; cl00742 688245010456 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 688245010457 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 688245010458 active site 688245010459 metal-binding site 688245010460 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 688245010461 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...; Region: Trunc_globin; cd00454 688245010462 apolar tunnel; other site 688245010463 heme binding site; other site 688245010464 dimerization interface; other site 688245010465 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 688245010466 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 688245010467 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010468 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245010469 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_7; cd08476 688245010470 putative effector binding pocket; other site 688245010471 putative dimerization interface; other site 688245010472 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 688245010473 Predicted permease; Region: FtsX; cl11418 688245010474 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 688245010475 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...; Region: metallo-dependent_hydrolases; cl00281 688245010476 active site 688245010477 Low molecular weight phosphatase family; Region: LMWPc; cd00115 688245010478 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 688245010479 active site 688245010480 Uncharacterized protein family (UPF0167); Region: UPF0167; cl01252 688245010481 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 688245010482 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 688245010483 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 688245010484 homotrimer interaction site; other site 688245010485 putative active site; other site 688245010486 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245010487 Amino acid permease; Region: AA_permease; pfam00324 688245010488 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010489 FAD dependent oxidoreductase; Region: DAO; pfam01266 688245010490 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245010491 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245010492 EamA-like transporter family; Region: EamA; cl01037 688245010493 EamA-like transporter family; Region: EamA; cl01037 688245010494 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 688245010495 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 688245010496 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 688245010497 catalytic loop; other site 688245010498 iron binding site; other site 688245010499 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 688245010500 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 alpha-; Region: HCP_like; cl14655 688245010501 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)...; Region: MopB_Formate-Dh-H; cd02753 688245010502 [4Fe-4S] binding site; other site 688245010503 molybdopterin cofactor binding site; other site 688245010504 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...; Region: MopB_CT_Fdh-Nap-like; cd00508 688245010505 molybdopterin cofactor binding site; other site 688245010506 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 688245010507 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 688245010508 putative dimer interface; other site 688245010509 [2Fe-2S] cluster binding site; other site 688245010510 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 688245010511 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 688245010512 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 688245010513 SLBB domain; Region: SLBB; pfam10531 688245010514 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 688245010515 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245010516 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010517 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 688245010518 dimerization interface; other site 688245010519 Domain of unknown function DUF59; Region: DUF59; cl00941 688245010520 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 688245010521 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 688245010522 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 688245010523 nucleophile elbow; other site 688245010524 Cache domain; Region: Cache_1; pfam02743 688245010525 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 connected by an extended linker. The...; Region: HAMP; cd06225 688245010526 dimerization interface; other site 688245010527 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010528 metal-binding site 688245010529 active site 688245010530 I-site; other site 688245010531 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 688245010532 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 688245010533 active site 688245010534 HIGH motif; other site 688245010535 KMSKS motif; other site 688245010536 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 688245010537 tRNA binding surface; other site 688245010538 anticodon binding site; other site 688245010539 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 688245010540 dimer interface; other site 688245010541 putative tRNA-binding site; other site 688245010542 Cytochrome c; Region: Cytochrom_C; cl11414 688245010543 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245010544 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 688245010545 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 688245010546 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 688245010547 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 688245010548 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 688245010549 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 688245010550 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 688245010551 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 688245010552 ScpA/B protein; Region: ScpA_ScpB; cl00598 688245010553 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 688245010554 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 688245010555 FeS/SAM binding site; other site 688245010556 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 688245010557 active site 688245010558 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...; Region: gram_neg_porins; cd00342 688245010559 trimer interface; other site 688245010560 eyelet of channel; other site 688245010561 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 688245010562 tetramerization interface; other site 688245010563 active site 688245010564 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 688245010565 putative substrate binding pocket; other site 688245010566 trimer interface; other site 688245010567 DTW domain; Region: DTW; cl01221 688245010568 Predicted membrane protein [Function unknown]; Region: COG4682 688245010569 yiaA/B two helix domain; Region: YiaAB; cl01759 688245010570 yiaA/B two helix domain; Region: YiaAB; cl01759 688245010571 potential frameshift: common BLAST hit: gi|120612490|ref|YP_972168.1| para-aminobenzoate synthase, subunit I 688245010572 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 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 688245010573 substrate-cofactor binding pocket; other site 688245010574 homodimer interface; other site 688245010575 pyridoxal 5'-phosphate binding site; other site 688245010576 catalytic residue; other site 688245010577 aminodeoxychorismate synthase; Provisional; Region: PRK07508 688245010578 chorismate binding enzyme; Region: Chorismate_bind; cl10555 688245010579 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245010580 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 688245010581 active site 688245010582 oligomerization interface; other site 688245010583 metal-binding site 688245010584 Pantoate-beta-alanine ligase; Region: PanC; cd00560 688245010585 pantoate--beta-alanine ligase; Region: panC; TIGR00018 688245010586 active site 688245010587 ATP-binding site; other site 688245010588 pantoate-binding site; other site 688245010589 HXXH motif; other site 688245010590 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 688245010591 putative active site; other site 688245010592 putative catalytic site; other site 688245010593 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 688245010594 Permease family; Region: Xan_ur_permease; cl00967 688245010595 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 688245010596 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 688245010597 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010598 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 688245010599 dimerization interface; other site 688245010600 diaminopimelate decarboxylase; Provisional; Region: PRK11165 688245010601 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 688245010602 active site 688245010603 pyridoxal 5'-phosphate (PLP) binding site; other site 688245010604 substrate binding site; other site 688245010605 catalytic residues; other site 688245010606 dimer interface; other site 688245010607 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245010608 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 688245010609 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010610 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 688245010611 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 688245010612 SecA binding site; other site 688245010613 Preprotein binding site; other site 688245010614 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 688245010615 GSH binding site; other site 688245010616 catalytic residues; other site 688245010617 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 688245010618 active site residue 688245010619 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 688245010620 catalytic core; other site 688245010621 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 688245010622 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 688245010623 C-terminal peptidase (prc); Region: prc; TIGR00225 688245010624 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 688245010625 protein binding site; other site 688245010626 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 688245010627 Catalytic dyad; other site 688245010628 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 688245010629 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...; Region: ThiF_MoeB_HesA_family; cd00757 688245010630 ATP binding site; other site 688245010631 substrate interface; other site 688245010632 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 688245010633 active site 688245010634 phosphorylation site 688245010635 intermolecular recognition site; other site 688245010636 dimerization interface; other site 688245010637 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 688245010638 active site 688245010639 phosphorylation site 688245010640 intermolecular recognition site; other site 688245010641 dimerization interface; other site 688245010642 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...; Region: LuxR_C_like; cd06170 688245010643 DNA binding residues 688245010644 dimerization interface; other site 688245010645 CHASE3 domain; Region: CHASE3; cl05000 688245010646 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 688245010647 Histidine kinase; Region: HisKA_3; pfam07730 688245010648 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 688245010649 ATP binding site; other site 688245010650 Mg2+ binding site; other site 688245010651 G-X-G motif; other site 688245010652 Putative phospholipid-binding domain; Region: BON; cl02771 688245010653 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; cl09206 688245010654 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 688245010655 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 688245010656 active site 688245010657 (T/H)XGH motif; other site 688245010658 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; cl12011 688245010659 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 688245010660 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 688245010661 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 688245010662 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 688245010663 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 688245010664 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 688245010665 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 688245010666 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245010667 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 688245010668 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 688245010669 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010670 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 688245010671 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 688245010672 NAD(P) binding site; other site 688245010673 catalytic residues; other site 688245010674 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 688245010675 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 688245010676 inhibitor site; inhibition site 688245010677 active site 688245010678 dimer interface; other site 688245010679 catalytic residue; other site 688245010680 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 688245010681 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved...; Region: MR_like_2; cd03327 688245010682 putative active site pocket; other site 688245010683 putative metal binding site; other site 688245010684 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 688245010685 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 688245010686 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 688245010687 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 688245010688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010689 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 688245010690 dimerization interface; other site 688245010691 transcriptional regulator; Provisional; Region: PRK10632 688245010692 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010693 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_6; cd08475 688245010694 putative effector binding pocket; other site 688245010695 putative dimerization interface; other site 688245010696 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 688245010697 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 688245010698 putative substrate translocation pore; other site 688245010699 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010700 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245010701 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245010702 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245010703 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245010704 DNA binding site 688245010705 FCD domain; Region: FCD; cl11656 688245010706 Dehydratase family; Region: ILVD_EDD; cl00340 688245010707 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 688245010708 cytochrome b6-f complex iron-sulfur subunit; Provisional; Region: PRK13474 688245010709 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 688245010710 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245010711 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010712 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 688245010713 putative dimerization interface; other site 688245010714 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 688245010715 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245010716 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...; Region: Sigma70_r4; cl01055 688245010717 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 688245010718 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 688245010719 Fatty acid desaturase; Region: FA_desaturase; pfam00487 688245010720 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 688245010721 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by...; Region: init_cond_enzymes; cd00827 688245010722 dimer interface; other site 688245010723 active site 688245010724 Protein of unknown function (DUF3532); Region: DUF3532; pfam12050 688245010725 PAS domain S-box; Region: sensory_box; TIGR00229 688245010726 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 688245010727 putative active site; other site 688245010728 heme pocket; other site 688245010729 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010730 metal-binding site 688245010731 active site 688245010732 I-site; other site 688245010733 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 688245010734 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 688245010735 Cu(I) binding site; other site 688245010736 UbiA prenyltransferase family; Region: UbiA; cl00337 688245010737 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 688245010738 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 688245010739 Subunit III/VIIa interface; other site 688245010740 Phospholipid binding site; other site 688245010741 Subunit I/III interface; other site 688245010742 Subunit III/VIb interface; other site 688245010743 Subunit III/VIa interface; other site 688245010744 Subunit III/Vb interface; other site 688245010745 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 688245010746 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 688245010747 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 688245010748 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 688245010749 Subunit I/III interface; other site 688245010750 D-pathway; other site 688245010751 Subunit I/VIIc interface; other site 688245010752 Subunit I/IV interface; other site 688245010753 Subunit I/II interface; other site 688245010754 Low-spin heme (heme a) binding site; other site 688245010755 Subunit I/VIIa interface; other site 688245010756 Subunit I/VIa interface; other site 688245010757 Dimer interface; other site 688245010758 Putative water exit pathway; other site 688245010759 Binuclear center (heme a3/CuB); other site 688245010760 K-pathway; other site 688245010761 Subunit I/Vb interface; other site 688245010762 Putative proton exit pathway; other site 688245010763 Subunit I/VIb interface; other site 688245010764 Subunit I/VIc interface; other site 688245010765 Electron transfer pathway; other site 688245010766 Subunit I/VIIIb interface; other site 688245010767 Subunit I/VIIb interface; other site 688245010768 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 688245010769 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 688245010770 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 688245010771 Cytochrome c [Energy production and conversion]; Region: COG3258 688245010772 Cytochrome c; Region: Cytochrom_C; cl11414 688245010773 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 688245010774 ligand binding site; other site 688245010775 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 688245010776 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; cl12011 688245010777 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245010778 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 688245010779 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 688245010780 putative active site; other site 688245010781 putative catalytic site; other site 688245010782 LysE type translocator; Region: LysE; cl00565 688245010783 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 688245010784 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 688245010785 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245010786 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 688245010787 Cytochrome c; Region: Cytochrom_C; cl11414 688245010788 Cytochrome c; Region: Cytochrom_C; cl11414 688245010789 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 688245010790 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...; Region: AAA; cd00009 688245010791 Walker A motif; other site 688245010792 ATP binding site; other site 688245010793 Walker B motif; other site 688245010794 arginine finger; other site 688245010795 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 688245010796 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 688245010797 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 688245010798 Surface antigen; Region: Bac_surface_Ag; cl03097 688245010799 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 688245010800 Family of unknown function (DUF490); Region: DUF490; pfam04357 688245010801 Uncharacterized BCR, COG1937; Region: DUF156; cl00846 688245010802 Cation efflux family; Region: Cation_efflux; cl00316 688245010803 Domain of unknown function (DU1801); Region: DUF1801; cl01838 688245010804 Chromate transporter; Region: Chromate_transp; cl00902 688245010805 Chromate transporter; Region: Chromate_transp; cl00902 688245010806 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 688245010807 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 688245010808 The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; Region: PBP2_LysR_opines_like; cd08415 688245010809 putative dimerization interface; other site 688245010810 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 688245010811 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 688245010812 putative active site; other site 688245010813 heme pocket; other site 688245010814 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010815 metal-binding site 688245010816 active site 688245010817 I-site; other site 688245010818 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010819 metal-binding site 688245010820 active site 688245010821 I-site; other site 688245010822 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245010823 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 trans-...; Region: HisKA; cl00080 688245010824 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 688245010825 Mg2+ binding site; other site 688245010826 G-X-G motif; other site 688245010827 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 688245010828 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 688245010829 active site 688245010830 phosphorylation site 688245010831 intermolecular recognition site; other site 688245010832 dimerization interface; other site 688245010833 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...; Region: trans_reg_C; cd00383 688245010834 DNA binding site 688245010835 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 688245010836 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245010837 Walker A/P-loop; other site 688245010838 ATP binding site; other site 688245010839 Q-loop/lid; other site 688245010840 ABC transporter signature motif; other site 688245010841 Walker B; other site 688245010842 D-loop; other site 688245010843 H-loop/switch region; other site 688245010844 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 688245010845 active site 688245010846 catalytic residues; other site 688245010847 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 688245010848 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 688245010849 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 C-...; Region: PDZ_serine_protease; cd00987 688245010850 protein binding site; other site 688245010851 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 688245010852 catalytic residues; other site 688245010853 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 688245010854 Permease family; Region: Xan_ur_permease; cl00967 688245010855 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 688245010856 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 688245010857 active site 688245010858 putative substrate binding pocket; other site 688245010859 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245010860 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245010861 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 688245010862 dimerization interface; other site 688245010863 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 688245010864 putative acyl-acceptor binding pocket; other site 688245010865 dihydroorotase; Provisional; Region: PRK07627 688245010866 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...; Region: metallo-dependent_hydrolases; cl00281 688245010867 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 688245010868 active site 688245010869 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 688245010870 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 688245010871 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 688245010872 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245010873 Uncharacterized protein family (UPF0081); Region: UPF0081; cl00525 688245010874 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 688245010875 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 688245010876 DNA photolyase; Region: DNA_photolyase; pfam00875 688245010877 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 688245010878 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; cl00086 688245010879 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 688245010880 putative binding surface; other site 688245010881 active site 688245010882 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 688245010883 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 688245010884 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 688245010885 ATP binding site; other site 688245010886 Mg2+ binding site; other site 688245010887 G-X-G motif; other site 688245010888 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 688245010889 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 688245010890 active site 688245010891 phosphorylation site 688245010892 intermolecular recognition site; other site 688245010893 dimerization interface; other site 688245010894 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245010895 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245010896 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 688245010897 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 688245010898 active site 688245010899 phosphorylation site 688245010900 intermolecular recognition site; other site 688245010901 dimerization interface; other site 688245010902 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 688245010903 active site 688245010904 phosphorylation site 688245010905 intermolecular recognition site; other site 688245010906 dimerization interface; other site 688245010907 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...; Region: rubredoxin; cd00730 688245010908 iron binding site; other site 688245010909 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 688245010910 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 688245010911 substrate binding site; other site 688245010912 ATP binding site; other site 688245010913 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 688245010914 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 688245010915 inhibitor-cofactor binding pocket; inhibition site 688245010916 pyridoxal 5'-phosphate binding site; other site 688245010917 catalytic residue; other site 688245010918 PhoD-like phosphatase; Region: PhoD; pfam09423 688245010919 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 688245010920 putative active site; other site 688245010921 putative metal binding site; other site 688245010922 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 688245010923 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 688245010924 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 688245010925 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 688245010926 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 688245010927 active site 688245010928 Cytochrome c; Region: Cytochrom_C; cl11414 688245010929 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 688245010930 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 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 688245010931 purine monophosphate binding site; other site 688245010932 dimer interface; other site 688245010933 putative catalytic residues; other site 688245010934 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 688245010935 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 688245010936 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245010937 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 688245010938 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...; Region: DUS_like_FMN; cd02801 688245010939 FMN binding site; other site 688245010940 active site 688245010941 catalytic residues; other site 688245010942 substrate binding site; other site 688245010943 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 688245010944 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 688245010945 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 688245010946 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 688245010947 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 688245010948 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 688245010949 active site 688245010950 phosphorylation site 688245010951 intermolecular recognition site; other site 688245010952 dimerization interface; other site 688245010953 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...; Region: LuxR_C_like; cd06170 688245010954 DNA binding residues 688245010955 dimerization interface; other site 688245010956 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 trans-...; Region: HisKA; cl00080 688245010957 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 688245010958 ATP binding site; other site 688245010959 Mg2+ binding site; other site 688245010960 G-X-G motif; other site 688245010961 Outer membrane efflux protein; Region: OEP; pfam02321 688245010962 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 688245010963 Outer membrane efflux protein; Region: OEP; pfam02321 688245010964 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 688245010965 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245010966 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 688245010967 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 688245010968 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 5-...; Region: QPRTase; cd01572 688245010969 dimerization interface; other site 688245010970 active site 688245010971 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...; Region: Nudix_Hydrolase; cl00447 688245010972 PAS fold; Region: PAS_4; pfam08448 688245010973 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 688245010974 putative active site; other site 688245010975 heme pocket; other site 688245010976 PAS domain S-box; Region: sensory_box; TIGR00229 688245010977 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 688245010978 putative active site; other site 688245010979 heme pocket; other site 688245010980 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245010981 metal-binding site 688245010982 active site 688245010983 I-site; other site 688245010984 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 688245010985 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 688245010986 dinuclear metal binding motif; other site 688245010987 RNA polymerase sigma factor; Provisional; Region: PRK12514 688245010988 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245010989 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...; Region: Sigma70_r4; cl01055 688245010990 Anti-sigma-K factor rskA; Region: RskA; cl02208 688245010991 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 688245010992 Moco binding site; other site 688245010993 metal coordination site; other site 688245010994 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 688245010995 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 688245010996 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 688245010997 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 688245010998 putative heme binding pocket; other site 688245010999 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 688245011000 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta...; Region: Arsenite_oxidase; cd02135 688245011001 putative FMN binding site; other site 688245011002 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011003 Integral membrane protein TerC family; Region: TerC; cl10468 688245011004 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 688245011005 Ligand Binding Site; other site 688245011006 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011007 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 688245011008 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 688245011009 dimerization interface; other site 688245011010 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 688245011011 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245011012 metal-binding site 688245011013 active site 688245011014 I-site; other site 688245011015 Protein of unknown function (DUF1428); Region: DUF1428; cl02319 688245011016 GTP-binding protein YchF; Reviewed; Region: PRK09601 688245011017 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 688245011018 G1 box; other site 688245011019 GTP/Mg2+ binding site; other site 688245011020 Switch I region; other site 688245011021 G2 box; other site 688245011022 Switch II region; other site 688245011023 G3 box; other site 688245011024 G4 box; other site 688245011025 G5 box; other site 688245011026 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 688245011027 IS2 transposase TnpB; Reviewed; Region: PRK09409 688245011028 Integrase core domain; Region: rve; cl01316 688245011029 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; cl01116 688245011030 C-terminal domain; Region: primase_Cterm; TIGR01613 688245011031 DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]; Region: MutL; COG0323 688245011032 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 688245011033 Restriction endonuclease; Region: Mrr_cat; cl00747 688245011034 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1483 688245011035 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]; Region: COG1743 688245011036 Protein of unknown function (DUF1156); Region: DUF1156; pfam06634 688245011037 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 688245011038 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 688245011039 ATP binding site; other site 688245011040 putative Mg++ binding site; other site 688245011041 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 688245011042 nucleotide binding region; other site 688245011043 ATP-binding site; other site 688245011044 Predicted transcriptional regulator [Transcription]; Region: COG2378 688245011045 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 688245011046 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 688245011047 MOSC domain; Region: MOSC; pfam03473 688245011048 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245011049 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 688245011050 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 688245011051 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...; Region: DsbA_DsbC_DsbG; cd03020 688245011052 dimerization domain; other site 688245011053 dimer interface; other site 688245011054 catalytic residues; other site 688245011055 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 688245011056 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 688245011057 enoyl-CoA hydratase; Provisional; Region: PRK05862 688245011058 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 688245011059 substrate binding site; other site 688245011060 oxyanion hole (OAH) forming residues; other site 688245011061 trimer interface; other site 688245011062 potential protein location (hypothetical protein CtCNB1_4057 [Comamonas testosteroni CNB-2]) that overlaps RNA (tRNA-M) 688245011063 benzoate transport; Region: 2A0115; TIGR00895 688245011064 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 688245011065 putative substrate translocation pore; other site 688245011066 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245011067 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011068 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 688245011069 substrate binding pocket; other site 688245011070 dimerization interface; other site 688245011071 benzoylformate decarboxylase; Reviewed; Region: PRK07092 688245011072 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 688245011073 PYR/PP interface; other site 688245011074 dimer interface; other site 688245011075 TPP binding site; other site 688245011076 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 688245011077 TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This...; Region: TPP_BFDC; cd02002 688245011078 TPP-binding site; other site 688245011079 dimer interface; other site 688245011080 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 688245011081 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011082 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 688245011083 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 688245011084 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 688245011085 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 688245011086 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011087 TOBE domain; Region: TOBE_2; cl01440 688245011088 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 688245011089 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...; Region: TM_PBP2; cd06261 688245011090 dimer interface; other site 688245011091 conserved gate region; other site 688245011092 putative PBP binding loops; other site 688245011093 ABC-ATPase subunit interface; other site 688245011094 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 688245011095 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011096 Walker A/P-loop; other site 688245011097 ATP binding site; other site 688245011098 Q-loop/lid; other site 688245011099 ABC transporter signature motif; other site 688245011100 Walker B; other site 688245011101 D-loop; other site 688245011102 H-loop/switch region; other site 688245011103 TOBE domain; Region: TOBE_2; cl01440 688245011104 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 688245011105 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 688245011106 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 688245011107 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 688245011108 FeS/SAM binding site; other site 688245011109 TRAM domain; Region: TRAM; cl01282 688245011110 NlpC/P60 family; Region: NLPC_P60; cl11438 688245011111 signal recognition particle protein; Provisional; Region: PRK10867 688245011112 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 688245011113 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 688245011114 GTP binding site; other site 688245011115 Signal peptide binding domain; Region: SRP_SPB; pfam02978 688245011116 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 688245011117 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 688245011118 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 trans...; Region: HisKA; cd00082 688245011119 dimer interface; other site 688245011120 phosphorylation site 688245011121 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 688245011122 ATP binding site; other site 688245011123 Mg2+ binding site; other site 688245011124 G-X-G motif; other site 688245011125 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 688245011126 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 688245011127 active site 688245011128 phosphorylation site 688245011129 intermolecular recognition site; other site 688245011130 dimerization interface; other site 688245011131 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...; Region: AAA; cd00009 688245011132 Walker A motif; other site 688245011133 ATP binding site; other site 688245011134 Walker B motif; other site 688245011135 arginine finger; other site 688245011136 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 688245011137 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 688245011138 amidase catalytic site; other site 688245011139 Zn binding residues; other site 688245011140 substrate binding site; other site 688245011141 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 688245011142 ATP cone domain; Region: ATP-cone; pfam03477 688245011143 Class I ribonucleotide reductase; Region: RNR_I; cd01679 688245011144 active site 688245011145 dimer interface; other site 688245011146 catalytic residues; other site 688245011147 effector binding site; other site 688245011148 R2 peptide binding site; other site 688245011149 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 688245011150 dimer interface; other site 688245011151 putative radical transfer pathway; other site 688245011152 diiron center; other site 688245011153 tyrosyl radical; other site 688245011154 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 688245011155 substrate binding site; other site 688245011156 ATP binding site; other site 688245011157 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 688245011158 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; cl12011 688245011159 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 688245011160 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 688245011161 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245011162 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245011163 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245011164 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 688245011165 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 688245011166 carboxyltransferase (CT) interaction site; other site 688245011167 biotinylation site; other site 688245011168 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...; Region: TlpA_like_family; cd02966 688245011169 catalytic residues; other site 688245011170 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 688245011171 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 688245011172 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245011173 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245011174 Domain of unknown function, DUF446; Region: DUF446; cl01187 688245011175 NeuB family; Region: NeuB; cl00496 688245011176 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 688245011177 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 688245011178 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 688245011179 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; cl12031 688245011180 Exoribonuclease R [Transcription]; Region: VacB; COG0557 688245011181 RNB domain; Region: RNB; pfam00773 688245011182 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 688245011183 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 688245011184 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 688245011185 shikimate binding site; other site 688245011186 NAD(P) binding site; other site 688245011187 Transglycosylase; Region: Transgly; cl07896 688245011188 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 includes...; Region: RuvC_resolvase; cd00529 688245011189 active site 688245011190 putative DNA-binding cleft; other site 688245011191 dimer interface; other site 688245011192 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 688245011193 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 688245011194 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 688245011195 cell division protein FtsZ; Validated; Region: PRK09330 688245011196 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...; Region: FtsZ_type1; cd02201 688245011197 nucleotide binding site; other site 688245011198 SulA interaction site; other site 688245011199 cell division protein FtsA; Region: ftsA; TIGR01174 688245011200 Cell division protein FtsA; Region: FtsA; cl11496 688245011201 Cell division protein FtsA; Region: FtsA; cl11496 688245011202 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 688245011203 Cell division protein FtsQ; Region: FtsQ; pfam03799 688245011204 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 688245011205 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 688245011206 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245011207 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 688245011208 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 688245011209 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245011210 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245011211 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 688245011212 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...; Region: GT1_MurG; cd03785 688245011213 active site 688245011214 homodimer interface; other site 688245011215 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 688245011216 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 688245011217 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245011218 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245011219 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 688245011220 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 688245011221 Mg++ binding site; other site 688245011222 putative catalytic motif; other site 688245011223 putative substrate binding site; other site 688245011224 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 688245011225 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 688245011226 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245011227 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 688245011228 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 688245011229 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 688245011230 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 688245011231 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 688245011232 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 688245011233 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245011234 Septum formation initiator; Region: DivIC; cl11433 688245011235 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; cl12011 688245011236 MraZ protein; Region: MraZ; pfam02381 688245011237 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 688245011238 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...; Region: AAA; cd00009 688245011239 Walker A motif; other site 688245011240 ATP binding site; other site 688245011241 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011242 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 688245011243 active site 688245011244 HslU subunit interaction site; other site 688245011245 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 688245011246 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 688245011247 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 688245011248 P-loop, Walker A motif; other site 688245011249 Base recognition motif; other site 688245011250 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 688245011251 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 688245011252 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 688245011253 DNA binding site 688245011254 Int/Topo IB signature motif; other site 688245011255 active site 688245011256 potential frameshift: common BLAST hit: gi|222112166|ref|YP_002554430.1| protein of unknown function DUF484 688245011257 Protein of unknown function, DUF484; Region: DUF484; cl01228 688245011258 Protein of unknown function, DUF484; Region: DUF484; cl01228 688245011259 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 688245011260 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 688245011261 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 688245011262 Transcriptional regulators [Transcription]; Region: MarR; COG1846 688245011263 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011264 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245011265 putative acyl-CoA dehydrogenase; Provisional; Region: PRK12341 688245011266 active site 688245011267 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 688245011268 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245011269 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011270 NAD(P) binding site; other site 688245011271 active site 688245011272 feruloyl-CoA synthase; Reviewed; Region: PRK08180 688245011273 enoyl-CoA hydratase; Provisional; Region: PRK08150 688245011274 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 688245011275 substrate binding site; other site 688245011276 oxyanion hole (OAH) forming residues; other site 688245011277 trimer interface; other site 688245011278 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...; Region: Nudix_Hydrolase; cl00447 688245011279 nudix motif; other site 688245011280 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245011281 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 688245011282 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; cl09940 688245011283 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 688245011284 active site 688245011285 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 688245011286 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 688245011287 FAD binding pocket; other site 688245011288 FAD binding motif; other site 688245011289 phosphate binding motif; other site 688245011290 NAD binding pocket; other site 688245011291 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 688245011292 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; cl11420 688245011293 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245011294 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 688245011295 N-terminal plug; other site 688245011296 ligand-binding site; other site 688245011297 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245011298 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; cl00047 688245011299 Cupin domain; Region: Cupin_2; cl09118 688245011300 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 688245011301 EamA-like transporter family; Region: EamA; cl01037 688245011302 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245011303 EamA-like transporter family; Region: EamA; cl01037 688245011304 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 688245011305 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 688245011306 putative substrate translocation pore; other site 688245011307 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 688245011308 amidase; Provisional; Region: PRK07056 688245011309 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; cl11426 688245011310 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245011311 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011312 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 688245011313 dimerization interface; other site 688245011314 cysteine synthases; Region: cysKM; TIGR01136 688245011315 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 688245011316 dimer interface; other site 688245011317 pyridoxal 5'-phosphate binding site; other site 688245011318 catalytic residue; other site 688245011319 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 688245011320 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245011321 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011322 Walker A/P-loop; other site 688245011323 ATP binding site; other site 688245011324 Q-loop/lid; other site 688245011325 ABC transporter signature motif; other site 688245011326 Walker B; other site 688245011327 D-loop; other site 688245011328 H-loop/switch region; other site 688245011329 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 688245011330 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 688245011331 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...; Region: LuxR_C_like; cl10457 688245011332 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245011333 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011334 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 688245011335 putative effector binding pocket; other site 688245011336 dimerization interface; other site 688245011337 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 688245011338 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 688245011339 NADP binding site; other site 688245011340 dimer interface; other site 688245011341 Uncharacterized conserved protein (DUF2164); Region: DUF2164; cl02278 688245011342 exonuclease subunit SbcD; Provisional; Region: PRK10966 688245011343 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 688245011344 active site 688245011345 metal-binding site 688245011346 DNA binding site 688245011347 Type 5 capsule protein repressor C terminal; Region: SbcD_C; pfam12320 688245011348 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011349 Walker A/P-loop; other site 688245011350 ATP binding site; other site 688245011351 Q-loop/lid; other site 688245011352 exonuclease subunit SbcC; Provisional; Region: PRK10246 688245011353 exonuclease subunit SbcC; Provisional; Region: PRK10246 688245011354 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011355 ABC transporter signature motif; other site 688245011356 Walker B; other site 688245011357 D-loop; other site 688245011358 H-loop/switch region; other site 688245011359 Intradiol dioxygenase supgroup. Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. They break the catechol C1-C2 bond and utilize Fe3+, as opposed to the...; Region: intradiol_dioxygenase_like; cd03457 688245011360 putative active site; other site 688245011361 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245011362 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245011363 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; cl09110 688245011364 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; cl09110 688245011365 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 688245011366 enoyl-CoA hydratase; Provisional; Region: PRK07511 688245011367 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 688245011368 substrate binding site; other site 688245011369 oxyanion hole (OAH) forming residues; other site 688245011370 trimer interface; other site 688245011371 Peptidase family M48; Region: Peptidase_M48; cl12018 688245011372 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 688245011373 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 688245011374 putative metal binding site; other site 688245011375 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 688245011376 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 688245011377 active site 688245011378 substrate binding pocket; other site 688245011379 dimer interface; other site 688245011380 ornithine cyclodeaminase; Validated; Region: PRK07589 688245011381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011382 Arginase family; Region: Arginase; cl00306 688245011383 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 688245011384 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 688245011385 Walker A/P-loop; other site 688245011386 ATP binding site; other site 688245011387 Q-loop/lid; other site 688245011388 ABC transporter signature motif; other site 688245011389 Walker B; other site 688245011390 D-loop; other site 688245011391 H-loop/switch region; other site 688245011392 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 688245011393 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...; Region: TM_PBP2; cd06261 688245011394 dimer interface; other site 688245011395 conserved gate region; other site 688245011396 putative PBP binding loops; other site 688245011397 ABC-ATPase subunit interface; other site 688245011398 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...; Region: TM_PBP2; cd06261 688245011399 dimer interface; other site 688245011400 conserved gate region; other site 688245011401 putative PBP binding loops; other site 688245011402 ABC-ATPase subunit interface; other site 688245011403 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245011404 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...; Region: PBPb; cd00134 688245011405 substrate binding pocket; other site 688245011406 membrane-bound complex binding site; other site 688245011407 hinge residues; other site 688245011408 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245011409 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011410 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 688245011411 dimerization interface; other site 688245011412 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245011413 DctM-like transporters; Region: DctM; pfam06808 688245011414 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; cl09110 688245011415 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245011416 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 688245011417 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011418 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245011419 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...; Region: PDR_like; cd06185 688245011420 FMN-binding pocket; other site 688245011421 flavin binding motif; other site 688245011422 phosphate binding motif; other site 688245011423 beta-alpha-beta structure motif; other site 688245011424 NAD binding pocket; other site 688245011425 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 688245011426 catalytic loop; other site 688245011427 iron binding site; other site 688245011428 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 688245011429 Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-...; Region: Rieske_RO_Alpha_VanA_DdmC; cd03532 688245011430 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 688245011431 alpha subunit interface; other site 688245011432 active site 688245011433 substrate binding site; other site 688245011434 Fe binding site; other site 688245011435 benzoate transport; Region: 2A0115; TIGR00895 688245011436 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 688245011437 putative substrate translocation pore; other site 688245011438 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011439 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)...; Region: Rieske; cl00938 688245011440 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 688245011441 iron-sulfur cluster; other site 688245011442 [2Fe-2S] cluster binding site; other site 688245011443 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 688245011444 alpha subunit interface; other site 688245011445 active site 688245011446 substrate binding site; other site 688245011447 Fe binding site; other site 688245011448 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 688245011449 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245011450 DNA binding site 688245011451 FCD domain; Region: FCD; cl11656 688245011452 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 688245011453 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 688245011454 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 688245011455 Walker A/P-loop; other site 688245011456 ATP binding site; other site 688245011457 Q-loop/lid; other site 688245011458 ABC transporter signature motif; other site 688245011459 Walker B; other site 688245011460 D-loop; other site 688245011461 H-loop/switch region; other site 688245011462 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...; Region: BFIT_BACH; cd03442 688245011463 Protein of unknown function, DUF583; Region: DUF583; cl09137 688245011464 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 688245011465 CoenzymeA binding site; other site 688245011466 subunit interaction site; other site 688245011467 PHB binding site; other site 688245011468 enoyl-CoA hydratase; Provisional; Region: PRK06688 688245011469 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 688245011470 substrate binding site; other site 688245011471 oxyanion hole (OAH) forming residues; other site 688245011472 trimer interface; other site 688245011473 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 688245011474 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; cl12031 688245011475 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; cl12031 688245011476 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 688245011477 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 688245011478 dimer interface; other site 688245011479 active site 688245011480 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 688245011481 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011482 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245011483 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245011484 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 688245011485 substrate binding site; other site 688245011486 oxyanion hole (OAH) forming residues; other site 688245011487 trimer interface; other site 688245011488 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 688245011489 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 688245011490 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 688245011491 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245011492 active site 688245011493 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245011494 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245011495 division inhibitor protein; Provisional; Region: slmA; PRK09480 688245011496 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245011497 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 688245011498 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245011499 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 trans-...; Region: HisKA; cd00082 688245011500 dimer interface; other site 688245011501 phosphorylation site 688245011502 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 688245011503 ATP binding site; other site 688245011504 Mg2+ binding site; other site 688245011505 G-X-G motif; other site 688245011506 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245011507 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 688245011508 active site 688245011509 phosphorylation site 688245011510 intermolecular recognition site; other site 688245011511 dimerization interface; other site 688245011512 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...; Region: trans_reg_C; cd00383 688245011513 DNA binding site 688245011514 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...; Region: AAK_NAGK-C; cd04250 688245011515 feedback inhibition sensing region; other site 688245011516 homohexameric interface; other site 688245011517 nucleotide binding site; other site 688245011518 N-acetyl-L-glutamate binding site; other site 688245011519 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...; Region: GT_MraY_like; cd06912 688245011520 Mg++ binding site; other site 688245011521 putative catalytic motif; other site 688245011522 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 688245011523 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 688245011524 putative ADP-binding pocket; other site 688245011525 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 688245011526 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 688245011527 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 688245011528 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 688245011529 active site 688245011530 homodimer interface; other site 688245011531 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 688245011532 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 688245011533 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 688245011534 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 688245011535 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 688245011536 dimer interface; other site 688245011537 motif 1; other site 688245011538 active site 688245011539 motif 2; other site 688245011540 motif 3; other site 688245011541 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 688245011542 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245011543 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 688245011544 TFIIB zinc-binding; Region: TF_Zn_Ribbon; pfam08271 688245011545 FAD dependent oxidoreductase TIGR03364; Region: HpnW_proposed 688245011546 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245011547 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 688245011548 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...; Region: TM_PBP2; cd06261 688245011549 dimer interface; other site 688245011550 conserved gate region; other site 688245011551 putative PBP binding loops; other site 688245011552 ABC-ATPase subunit interface; other site 688245011553 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...; Region: TM_PBP2; cd06261 688245011554 dimer interface; other site 688245011555 conserved gate region; other site 688245011556 putative PBP binding loops; other site 688245011557 ABC-ATPase subunit interface; other site 688245011558 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 688245011559 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245011560 Walker A/P-loop; other site 688245011561 ATP binding site; other site 688245011562 Q-loop/lid; other site 688245011563 ABC transporter signature motif; other site 688245011564 Walker B; other site 688245011565 D-loop; other site 688245011566 H-loop/switch region; other site 688245011567 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 688245011568 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 688245011569 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 688245011570 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011571 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 688245011572 dimerization interface; other site 688245011573 Cupin domain; Region: Cupin_2; cl09118 688245011574 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 688245011575 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 688245011576 substrate binding site; other site 688245011577 tetramer interface; other site 688245011578 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011579 active site 688245011580 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011581 NAD(P) binding site; other site 688245011582 active site 688245011583 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 688245011584 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 688245011585 NAD binding site; other site 688245011586 substrate binding site; other site 688245011587 homodimer interface; other site 688245011588 active site 688245011589 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 688245011590 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 688245011591 Putative phospholipid-binding domain; Region: BON; cl02771 688245011592 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 688245011593 putative peptidoglycan binding site; other site 688245011594 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 688245011595 UDP-glucose 4-epimerase; Region: PLN02240 688245011596 NAD binding site; other site 688245011597 homodimer interface; other site 688245011598 active site 688245011599 substrate binding site; other site 688245011600 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 688245011601 active site residue 688245011602 Protein of unknown function DUF45; Region: DUF45; cl00636 688245011603 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 688245011604 putative acyl-acceptor binding pocket; other site 688245011605 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 688245011606 active site 688245011607 motif I; other site 688245011608 motif II; other site 688245011609 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 688245011610 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 688245011611 dimer interface; other site 688245011612 active site 688245011613 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 688245011614 dimer interface; other site 688245011615 active site 1 688245011616 active site 2 688245011617 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 688245011618 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 688245011619 putative active site; other site 688245011620 catalytic triad; other site 688245011621 putative dimer interface; other site 688245011622 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 688245011623 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 688245011624 Transporter associated domain; Region: CorC_HlyC; pfam03471 688245011625 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245011626 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245011627 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011628 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 688245011629 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 688245011630 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 688245011631 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 688245011632 cofactor binding site; other site 688245011633 metal-binding site 688245011634 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 688245011635 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 688245011636 Mechanosensitive ion channel; Region: MS_channel; pfam00924 688245011637 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 688245011638 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245011639 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 688245011640 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 688245011641 octamerization interface; other site 688245011642 diferric-oxygen binding site; other site 688245011643 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245011644 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 688245011645 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 688245011646 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 688245011647 FAD binding pocket; other site 688245011648 FAD binding motif; other site 688245011649 phosphate binding motif; other site 688245011650 NAD binding pocket; other site 688245011651 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011652 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 688245011653 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 688245011654 N-terminal plug; other site 688245011655 ligand-binding site; other site 688245011656 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245011657 bifunctional enterobactin receptor/adhesin protein; Provisional; Region: PRK13486 688245011658 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 688245011659 N-terminal plug; other site 688245011660 ligand-binding site; other site 688245011661 lytic murein transglycosylase; Provisional; Region: PRK11619 688245011662 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 catalyze...; Region: LT_GEWL; cd00254 688245011663 N-acetyl-D-glucosamine binding site; other site 688245011664 catalytic residue; other site 688245011665 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 688245011666 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 688245011667 Ligand Binding Site; other site 688245011668 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245011669 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)...; Region: GST_N_1; cd03043 688245011670 putative C-terminal domain interface; other site 688245011671 putative GSH binding site (G-site); other site 688245011672 putative dimer interface; other site 688245011673 GST_C family, unknown subfamily 3; composed of uncharacterized 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 endogenous...; Region: GST_C_3; cd03194 688245011674 putative N-terminal domain interface; other site 688245011675 putative dimer interface; other site 688245011676 putative substrate binding pocket (H-site); other site 688245011677 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 688245011678 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 688245011679 active site 688245011680 NTP binding site; other site 688245011681 metal binding triad; metal-binding site 688245011682 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245011683 Zn2+ binding site; other site 688245011684 Mg2+ binding site; other site 688245011685 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 688245011686 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 688245011687 NAD binding site; other site 688245011688 substrate binding site; other site 688245011689 catalytic Zn binding site; other site 688245011690 tetramer interface; other site 688245011691 structural Zn binding site; other site 688245011692 thioredoxin 2; Provisional; Region: PRK10996 688245011693 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 688245011694 catalytic residues; other site 688245011695 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 688245011696 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 688245011697 Uncharacterized conserved protein [Function unknown]; Region: COG1565 688245011698 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 688245011699 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 688245011700 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011701 NAD(P) binding site; other site 688245011702 active site 688245011703 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 688245011704 active site 688245011705 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 688245011706 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...; Region: Alpha_ANH_like_II; cd01993 688245011707 Ligand Binding Site; other site 688245011708 Protein of unknown function (DUF2501); Region: DUF2501; cl08197 688245011709 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 688245011710 catalytic core; other site 688245011711 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 688245011712 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 688245011713 dimer interface; other site 688245011714 active site 688245011715 pyridoxal 5'-phosphate (PLP) binding site; other site 688245011716 substrate binding site; other site 688245011717 catalytic residue; other site 688245011718 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245011719 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245011720 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245011721 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 688245011722 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 688245011723 YhhN-like protein; Region: YhhN; cl01505 688245011724 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 688245011725 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 688245011726 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 688245011727 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; cl11391 688245011728 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 688245011729 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 688245011730 MgtC family; Region: MgtC; cl12207 688245011731 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 688245011732 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...; Region: AAA; cd00009 688245011733 Walker A motif; other site 688245011734 ATP binding site; other site 688245011735 Walker B motif; other site 688245011736 arginine finger; other site 688245011737 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 688245011738 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...; Region: PRX_BCP; cd03017 688245011739 catalytic triad; other site 688245011740 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 688245011741 RuvA N terminal domain; Region: RuvA_N; pfam01330 688245011742 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 688245011743 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 688245011744 PhoH-like protein; Region: PhoH; cl12134 688245011745 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 688245011746 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 688245011747 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 688245011748 ATP binding site; other site 688245011749 Mg2+ binding site; other site 688245011750 G-X-G motif; other site 688245011751 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 688245011752 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 688245011753 active site 688245011754 phosphorylation site 688245011755 intermolecular recognition site; other site 688245011756 dimerization interface; other site 688245011757 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...; Region: LuxR_C_like; cd06170 688245011758 DNA binding residues 688245011759 dimerization interface; other site 688245011760 Domain of unknown function (DUF336); Region: DUF336; cl01249 688245011761 Surface antigen; Region: Surface_Ag_2; cl01155 688245011762 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 688245011763 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 688245011764 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 688245011765 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 688245011766 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 688245011767 ATP binding site; other site 688245011768 Mg++ binding site; other site 688245011769 motif III; other site 688245011770 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 688245011771 nucleotide binding region; other site 688245011772 ATP-binding site; other site 688245011773 DbpA RNA binding domain; Region: DbpA; pfam03880 688245011774 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245011775 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245011776 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245011777 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...; Region: Dtyr_deacylase; cd00563 688245011778 putative active site; other site 688245011779 dimerization interface; other site 688245011780 putative tRNAtyr binding site; other site 688245011781 Cation efflux family; Region: Cation_efflux; cl00316 688245011782 PAS fold; Region: PAS_4; pfam08448 688245011783 PAS domain S-box; Region: sensory_box; TIGR00229 688245011784 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 688245011785 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245011786 metal-binding site 688245011787 active site 688245011788 I-site; other site 688245011789 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 688245011790 AMP nucleosidase; Provisional; Region: PRK08292 688245011791 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 688245011792 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 688245011793 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245011794 metal-binding site 688245011795 active site 688245011796 I-site; other site 688245011797 choline dehydrogenase; Validated; Region: PRK02106 688245011798 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 688245011799 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 688245011800 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 688245011801 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245011802 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 688245011803 enoyl-CoA hydratase; Provisional; Region: PRK06563 688245011804 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 688245011805 substrate binding site; other site 688245011806 oxyanion hole (OAH) forming residues; other site 688245011807 trimer interface; other site 688245011808 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 688245011809 Beta-lactamase; Region: Beta-lactamase; cl01009 688245011810 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011811 OsmC-like protein; Region: OsmC; cl00767 688245011812 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 688245011813 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 688245011814 Phosphotransferase enzyme family; Region: APH; pfam01636 688245011815 HTH-type transcriptional regulator RutR; Provisional; Region: PRK15008 688245011816 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245011817 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 688245011818 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245011819 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 688245011820 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 688245011821 DNA binding residues 688245011822 dimer interface; other site 688245011823 [2Fe-2S] cluster binding site; other site 688245011824 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 688245011825 homotrimer interaction site; other site 688245011826 putative active site; other site 688245011827 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 688245011828 heat shock protein 90; Provisional; Region: PRK05218 688245011829 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 688245011830 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 688245011831 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 688245011832 RNA binding surface; other site 688245011833 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 688245011834 active site 688245011835 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 688245011836 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 688245011837 ligand binding site; other site 688245011838 flexible hinge region; other site 688245011839 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011840 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 688245011841 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245011842 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245011843 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 688245011844 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245011845 Walker A/P-loop; other site 688245011846 ATP binding site; other site 688245011847 Q-loop/lid; other site 688245011848 ABC transporter signature motif; other site 688245011849 Walker B; other site 688245011850 D-loop; other site 688245011851 H-loop/switch region; other site 688245011852 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 688245011853 TM-ABC transporter signature motif; other site 688245011854 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 688245011855 TM-ABC transporter signature motif; other site 688245011856 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 688245011857 putative ligand binding site; other site 688245011858 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 688245011859 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245011860 Walker A/P-loop; other site 688245011861 ATP binding site; other site 688245011862 Q-loop/lid; other site 688245011863 ABC transporter signature motif; other site 688245011864 Walker B; other site 688245011865 D-loop; other site 688245011866 H-loop/switch region; other site 688245011867 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245011868 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 688245011869 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 688245011870 Cyclopropane-fatty-acyl-phospholipid synthase; Region: CMAS; pfam02353 688245011871 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 688245011872 S-adenosylmethionine binding site; other site 688245011873 Predicted aminopeptidase (DUF2265); Region: DUF2265; cl01778 688245011874 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 688245011875 Sulfatase; Region: Sulfatase; cl10460 688245011876 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...; Region: TM_PBP2; cd06261 688245011877 dimer interface; other site 688245011878 conserved gate region; other site 688245011879 putative PBP binding loops; other site 688245011880 ABC-ATPase subunit interface; other site 688245011881 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245011882 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245011883 Walker A/P-loop; other site 688245011884 ATP binding site; other site 688245011885 Q-loop/lid; other site 688245011886 ABC transporter signature motif; other site 688245011887 Walker B; other site 688245011888 D-loop; other site 688245011889 H-loop/switch region; other site 688245011890 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 688245011891 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 688245011892 nucleoside/Zn binding site; other site 688245011893 dimer interface; other site 688245011894 catalytic motif; other site 688245011895 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 688245011896 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 688245011897 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 688245011898 flavanone-3-hydroxylase; Provisional; Region: PLN03176 688245011899 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 688245011900 Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a...; Region: ACBP; cl00221 688245011901 acyl-CoA binding pocket; other site 688245011902 CoA binding site; other site 688245011903 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...; Region: gram_neg_porins; cd00342 688245011904 trimer interface; other site 688245011905 eyelet of channel; other site 688245011906 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 688245011907 NADP binding site; other site 688245011908 dimer interface; other site 688245011909 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 688245011910 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 688245011911 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245011912 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 688245011913 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 688245011914 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 688245011915 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245011916 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 688245011917 putative ligand binding site; other site 688245011918 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...; Region: MopB_3; cd02766 688245011919 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 688245011920 putative [4Fe-4S] binding site; other site 688245011921 putative molybdopterin cofactor binding site; other site 688245011922 Molybdopterin-Binding, C-terminal (MopB_CT) 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-; Region: MopB_CT; cl09929 688245011923 molybdopterin cofactor binding site; other site 688245011924 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 688245011925 Cache domain; Region: Cache_1; pfam02743 688245011926 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245011927 metal-binding site 688245011928 active site 688245011929 I-site; other site 688245011930 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 688245011931 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245011932 Cytochrome c; Region: Cytochrom_C; cl11414 688245011933 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_3; cd06151 688245011934 homotrimer interaction site; other site 688245011935 putative active site; other site 688245011936 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 688245011937 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 688245011938 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...; Region: metallo-dependent_hydrolases; cl00281 688245011939 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 688245011940 Isochorismatase family; Region: Isochorismatase; pfam00857 688245011941 catalytic triad; other site 688245011942 dimer interface; other site 688245011943 conserved cis-peptide bond; other site 688245011944 Pirin-related protein [General function prediction only]; Region: COG1741 688245011945 Cupin domain; Region: Cupin_2; cl09118 688245011946 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 688245011947 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011948 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 688245011949 dimerization interface; other site 688245011950 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 688245011951 GumN protein; Region: GumN; cl12050 688245011952 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 688245011953 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011954 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245011955 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245011956 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 688245011957 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 688245011958 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 688245011959 Putative ammonia monooxygenase; Region: AmoA; pfam05145 688245011960 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 688245011961 Protein of unknown function, DUF399; Region: DUF399; cl01139 688245011962 PAS domain S-box; Region: sensory_box; TIGR00229 688245011963 PAS fold; Region: PAS_3; pfam08447 688245011964 PAS domain S-box; Region: sensory_box; TIGR00229 688245011965 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 688245011966 putative active site; other site 688245011967 heme pocket; other site 688245011968 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 688245011969 metal-binding site 688245011970 active site 688245011971 I-site; other site 688245011972 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 688245011973 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 688245011974 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 688245011975 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 688245011976 putative active site; other site 688245011977 putative substrate binding site; other site 688245011978 putative cosubstrate binding site; other site 688245011979 catalytic site; other site 688245011980 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 688245011981 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245011982 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 688245011983 dimerization interface; other site 688245011984 substrate binding pocket; other site 688245011985 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 688245011986 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245011987 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 688245011988 putative ligand binding site; other site 688245011989 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 688245011990 FAD binding domain; Region: FAD_binding_4; pfam01565 688245011991 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 688245011992 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 688245011993 pyridoxal 5'-phosphate binding pocket; other site 688245011994 catalytic residue; other site 688245011995 Pseudomonas-type; Region: PC_PLC; TIGR03396 688245011996 Phosphoesterase family; Region: Phosphoesterase; cl10627 688245011997 Domain of unknown function (DUF756); Region: DUF756; pfam05506 688245011998 Domain of unknown function (DUF756); Region: DUF756; pfam05506 688245011999 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 688245012000 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 688245012001 Outer membrane efflux protein; Region: OEP; pfam02321 688245012002 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 688245012003 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 688245012004 active site 688245012005 phosphorylation site 688245012006 intermolecular recognition site; other site 688245012007 dimerization interface; other site 688245012008 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...; Region: trans_reg_C; cd00383 688245012009 DNA binding site 688245012010 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 688245012011 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 connected by an extended linker. The...; Region: HAMP; cl01054 688245012012 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 trans-...; Region: HisKA; cd00082 688245012013 dimer interface; other site 688245012014 phosphorylation site 688245012015 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 688245012016 ATP binding site; other site 688245012017 G-X-G motif; other site 688245012018 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 688245012019 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 688245012020 putative ligand binding residues; other site 688245012021 enterobactin receptor protein; Provisional; Region: PRK13483 688245012022 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 688245012023 N-terminal plug; other site 688245012024 ligand-binding site; other site 688245012025 Protein of unknown function (DUF445); Region: DUF445; pfam04286 688245012026 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 688245012027 Outer membrane efflux protein; Region: OEP; pfam02321 688245012028 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 688245012029 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 688245012030 DXD motif; other site 688245012031 DNA polymerase II large subunit; Provisional; Region: PRK14714 688245012032 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 688245012033 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 688245012034 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 688245012035 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 688245012036 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 688245012037 heme-binding site; other site 688245012038 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 688245012039 FAD binding pocket; other site 688245012040 FAD binding motif; other site 688245012041 phosphate binding motif; other site 688245012042 beta-alpha-beta structure motif; other site 688245012043 NAD binding pocket; other site 688245012044 Heme binding pocket; other site 688245012045 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 688245012046 GAF domain; Region: GAF; cl00853 688245012047 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...; Region: AAA; cd00009 688245012048 Walker A motif; other site 688245012049 ATP binding site; other site 688245012050 Walker B motif; other site 688245012051 arginine finger; other site 688245012052 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245012053 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 688245012054 pyridoxal 5'-phosphate binding pocket; other site 688245012055 catalytic residue; other site 688245012056 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 688245012057 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 688245012058 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245012059 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 688245012060 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 688245012061 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component); Region: sucB; TIGR01347 688245012062 carboxyltransferase (CT) interaction site; other site 688245012063 biotinylation site; other site 688245012064 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 688245012065 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 688245012066 acyl-CoA synthetase; Validated; Region: PRK06178 688245012067 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245012068 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245012069 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245012070 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245012071 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 688245012072 putative ligand binding site; other site 688245012073 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 688245012074 pyridoxal 5'-phosphate (PLP) binding site; other site 688245012075 catalytic residue; other site 688245012076 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 688245012077 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 688245012078 Walker A motif; other site 688245012079 ATP binding site; other site 688245012080 Walker B motif; other site 688245012081 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 688245012082 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 688245012083 Walker A motif; other site 688245012084 ATP binding site; other site 688245012085 Walker B motif; other site 688245012086 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 688245012087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012088 Putative phospholipid-binding domain; Region: BON; cl02771 688245012089 Putative phospholipid-binding domain; Region: BON; cl02771 688245012090 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 688245012091 dimer interface; other site 688245012092 active site 688245012093 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 688245012094 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 688245012095 putative chaperone; Provisional; Region: PRK11678 688245012096 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 688245012097 OsmC-like protein; Region: OsmC; cl00767 688245012098 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 688245012099 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_15; cd08492 688245012100 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...; Region: TM_PBP2; cd06261 688245012101 dimer interface; other site 688245012102 conserved gate region; other site 688245012103 putative PBP binding loops; other site 688245012104 ABC-ATPase subunit interface; other site 688245012105 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...; Region: TM_PBP2; cl00427 688245012106 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 688245012107 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245012108 Walker A/P-loop; other site 688245012109 ATP binding site; other site 688245012110 Q-loop/lid; other site 688245012111 ABC transporter signature motif; other site 688245012112 Walker B; other site 688245012113 D-loop; other site 688245012114 H-loop/switch region; other site 688245012115 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 688245012116 Walker A/P-loop; other site 688245012117 ATP binding site; other site 688245012118 Q-loop/lid; other site 688245012119 ABC transporter signature motif; other site 688245012120 Walker B; other site 688245012121 D-loop; other site 688245012122 H-loop/switch region; other site 688245012123 Luciferase-like monooxygenase; Region: Bac_luciferase; pfam00296 688245012124 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 688245012125 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245012126 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 688245012127 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245012128 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; cl09110 688245012129 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 688245012130 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 688245012131 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 688245012132 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 688245012133 alphaNTD homodimer interface; other site 688245012134 alphaNTD - beta interaction site; other site 688245012135 alphaNTD - beta' interaction site; other site 688245012136 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 688245012137 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 688245012138 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 688245012139 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 688245012140 RNA binding surface; other site 688245012141 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 688245012142 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 688245012143 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 688245012144 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 688245012145 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 688245012146 eubacterial secY protein; Region: SecY; pfam00344 688245012147 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 688245012148 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...; Region: Ribosomal_L30; cd01658 688245012149 23S rRNA binding site; other site 688245012150 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 688245012151 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 688245012152 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 688245012153 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 688245012154 5S rRNA interface; other site 688245012155 23S rRNA interface; other site 688245012156 L5 interface; other site 688245012157 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 688245012158 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 688245012159 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 688245012160 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 688245012161 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 688245012162 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 688245012163 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 688245012164 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 688245012165 KOW motif; Region: KOW; cl00354 688245012166 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 688245012167 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 688245012168 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 688245012169 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012170 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 688245012171 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 688245012172 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245012173 Coenzyme A binding pocket; other site 688245012174 glycerol kinase; Provisional; Region: glpK; PRK00047 688245012175 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 688245012176 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 688245012177 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-...; Region: MIP; cl00200 688245012178 amphipathic channel; other site 688245012179 Asn-Pro-Ala signature motifs; other site 688245012180 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 688245012181 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 688245012182 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012183 UbiA prenyltransferase family; Region: UbiA; cl00337 688245012184 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 688245012185 active site 688245012186 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 688245012187 dimerization interface; other site 688245012188 DPS ferroxidase diiron center; other site 688245012189 ion pore; other site 688245012190 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 688245012191 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012192 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 688245012193 dimerization interface; other site 688245012194 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 688245012195 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 four-...; Region: RecG_wedge_OBF; cd04488 688245012196 generic binding surface II; other site 688245012197 ssDNA binding site; other site 688245012198 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 688245012199 ATP binding site; other site 688245012200 putative Mg++ binding site; other site 688245012201 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 688245012202 nucleotide binding region; other site 688245012203 ATP-binding site; other site 688245012204 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 688245012205 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 688245012206 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 688245012207 Zn2+ binding site; other site 688245012208 Mg2+ binding site; other site 688245012209 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 688245012210 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 688245012211 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 688245012212 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 688245012213 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 688245012214 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...; Region: trans_reg_C; cd00383 688245012215 DNA binding site 688245012216 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 688245012217 active site 688245012218 ribulose/triose binding site; other site 688245012219 phosphate binding site; other site 688245012220 substrate (anthranilate) binding pocket; other site 688245012221 product (indole) binding pocket; other site 688245012222 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 688245012223 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 688245012224 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 688245012225 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 688245012226 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 688245012227 glutamine binding; other site 688245012228 catalytic triad; other site 688245012229 Chorismate mutase type II; Region: CM_2; cl00693 688245012230 anthranilate synthase component I; Provisional; Region: PRK13565 688245012231 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 688245012232 chorismate binding enzyme; Region: Chorismate_bind; cl10555 688245012233 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 688245012234 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 688245012235 spermidine synthase; Provisional; Region: PRK00811 688245012236 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; cl12011 688245012237 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 688245012238 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 688245012239 motif II; other site 688245012240 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...; Region: RPE; cd00429 688245012241 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 688245012242 substrate binding site; other site 688245012243 hexamer interface; other site 688245012244 metal-binding site 688245012245 Protein of unknown function (DUF525); Region: DUF525; cl01119 688245012246 Site-specific recombinase [DNA replication, recombination, and repair]; Region: COG4389 688245012247 Site-specific recombinase; Region: SpecificRecomb; pfam10136 688245012248 thiamine monophosphate kinase; Provisional; Region: PRK05731 688245012249 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 688245012250 ATP binding site; other site 688245012251 dimerization interface; other site 688245012252 conserved hypothetical protein; Region: TIGR02231 688245012253 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 688245012254 tetramer interfaces; other site 688245012255 binuclear metal-binding site; other site 688245012256 Competence-damaged protein; Region: CinA; cl00666 688245012257 Predicted membrane protein [Function unknown]; Region: COG4655 688245012258 Predicted membrane protein (DUF2134); Region: DUF2134; pfam09977 688245012259 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 688245012260 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 688245012261 binding surface 688245012262 TPR motif; other site 688245012263 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245012264 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 688245012265 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 688245012266 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...; Region: VirB11-like_ATPase; cd01130 688245012267 ATP binding site; other site 688245012268 Walker A motif; other site 688245012269 hexamer interface; other site 688245012270 Walker B motif; other site 688245012271 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245012272 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 688245012273 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 688245012274 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 688245012275 SAF domain; Region: SAF; cl00555 688245012276 TadE-like protein; Region: TadE; pfam07811 688245012277 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 688245012278 non-specific DNA binding site; other site 688245012279 salt bridge; other site 688245012280 sequence-specific DNA binding site; other site 688245012281 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 688245012282 SEC-C motif; Region: SEC-C; cl12132 688245012283 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 688245012284 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...; Region: GltS_FMN; cd02808 688245012285 active site 688245012286 FMN binding site; other site 688245012287 substrate binding site; other site 688245012288 3Fe-4S cluster binding site; other site 688245012289 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 688245012290 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 688245012291 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 688245012292 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 688245012293 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 688245012294 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 trans-...; Region: HisKA; cl00080 688245012295 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 688245012296 ATP binding site; other site 688245012297 Mg2+ binding site; other site 688245012298 G-X-G motif; other site 688245012299 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 688245012300 active site 688245012301 phosphorylation site 688245012302 intermolecular recognition site; other site 688245012303 dimerization interface; other site 688245012304 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 688245012305 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 688245012306 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245012307 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 688245012308 active site 688245012309 phosphorylation site 688245012310 intermolecular recognition site; other site 688245012311 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...; Region: LuxR_C_like; cd06170 688245012312 DNA binding residues 688245012313 dimerization interface; other site 688245012314 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 688245012315 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 688245012316 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 688245012317 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245012318 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 688245012319 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012320 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245012321 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245012322 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245012323 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012324 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245012325 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 688245012326 Cytochrome P450; Region: p450; cl12078 688245012327 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245012328 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-...; Region: PDR_like; cd06185 688245012329 FMN-binding pocket; other site 688245012330 flavin binding motif; other site 688245012331 phosphate binding motif; other site 688245012332 beta-alpha-beta structure motif; other site 688245012333 NAD binding pocket; other site 688245012334 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 688245012335 catalytic loop; other site 688245012336 iron binding site; other site 688245012337 UreD urease accessory protein; Region: UreD; cl00530 688245012338 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 688245012339 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 688245012340 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 688245012341 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 688245012342 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 688245012343 Walker A/P-loop; other site 688245012344 ATP binding site; other site 688245012345 Q-loop/lid; other site 688245012346 ABC transporter signature motif; other site 688245012347 Walker B; other site 688245012348 D-loop; other site 688245012349 H-loop/switch region; other site 688245012350 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 688245012351 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 688245012352 Walker A/P-loop; other site 688245012353 ATP binding site; other site 688245012354 Q-loop/lid; other site 688245012355 ABC transporter signature motif; other site 688245012356 Walker B; other site 688245012357 D-loop; other site 688245012358 H-loop/switch region; other site 688245012359 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 688245012360 TM-ABC transporter signature motif; other site 688245012361 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 688245012362 TM-ABC transporter signature motif; other site 688245012363 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245012364 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 688245012365 putative ligand binding site; other site 688245012366 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 688245012367 ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CbiK; COG5266 688245012368 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 688245012369 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 688245012370 N-terminal plug; other site 688245012371 ligand-binding site; other site 688245012372 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 688245012373 alpha-gamma subunit interface; other site 688245012374 beta-gamma subunit interface; other site 688245012375 HupE / UreJ protein; Region: HupE_UreJ; cl01011 688245012376 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...; Region: Urease_beta; cd00407 688245012377 gamma-beta subunit interface; other site 688245012378 alpha-beta subunit interface; other site 688245012379 LysE type translocator; Region: LysE; cl00565 688245012380 urease subunit alpha; Reviewed; Region: ureC; PRK13207 688245012381 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 688245012382 subunit interactions; other site 688245012383 active site 688245012384 flap region; other site 688245012385 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 688245012386 putative active site pocket; other site 688245012387 dimerization interface; other site 688245012388 putative catalytic residue; other site 688245012389 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 C...; Region: UreE; cd00571 688245012390 dimer interface; other site 688245012391 catalytic residues; other site 688245012392 UreF; Region: UreF; cl00531 688245012393 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 688245012394 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 688245012395 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 688245012396 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245012397 Coenzyme A binding pocket; other site 688245012398 NeuB family; Region: NeuB; cl00496 688245012399 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 688245012400 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 688245012401 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 688245012402 PIN domain; Region: PIN; cl09128 688245012403 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 688245012404 THUMP domain; Region: THUMP; cl12076 688245012405 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; cl12011 688245012406 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 688245012407 dimer interface; other site 688245012408 putative tRNA-binding site; other site 688245012409 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 688245012410 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl01426 688245012411 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 688245012412 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 688245012413 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 688245012414 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 688245012415 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 688245012416 Walker A/P-loop; other site 688245012417 ATP binding site; other site 688245012418 Q-loop/lid; other site 688245012419 ABC transporter signature motif; other site 688245012420 Walker B; other site 688245012421 D-loop; other site 688245012422 H-loop/switch region; other site 688245012423 OstA-like protein; Region: OstA; cl00844 688245012424 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 688245012425 catalytic residues; other site 688245012426 hinge region; other site 688245012427 alpha helical domain; other site 688245012428 Sporulation related domain; Region: SPOR; cl10051 688245012429 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 688245012430 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 688245012431 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 688245012432 active site 688245012433 HIGH motif; other site 688245012434 KMSK motif region; other site 688245012435 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 688245012436 tRNA binding surface; other site 688245012437 anticodon binding site; other site 688245012438 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 688245012439 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245012440 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012441 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 688245012442 putative effector binding pocket; other site 688245012443 dimerization interface; other site 688245012444 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 688245012445 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 688245012446 ATP binding site; other site 688245012447 G-X-G motif; other site 688245012448 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245012449 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 688245012450 active site 688245012451 phosphorylation site 688245012452 intermolecular recognition site; other site 688245012453 dimerization interface; other site 688245012454 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...; Region: trans_reg_C; cd00383 688245012455 DNA binding site 688245012456 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 688245012457 active site 688245012458 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 688245012459 active site 1 688245012460 dimer interface; other site 688245012461 hexamer interface; other site 688245012462 active site 2 688245012463 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 688245012464 active site 1 688245012465 dimer interface; other site 688245012466 hexamer interface; other site 688245012467 active site 2 688245012468 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 688245012469 putative active site; other site 688245012470 putative dimer interface; other site 688245012471 glutathione synthetase; Provisional; Region: PRK05246 688245012472 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 688245012473 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245012474 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 688245012475 Permease family; Region: Xan_ur_permease; cl00967 688245012476 K+ potassium transporter; Region: K_trans; cl01227 688245012477 potassium uptake protein; Region: kup; TIGR00794 688245012478 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 688245012479 Glutamate-cysteine ligase; Region: GshA; pfam08886 688245012480 Cation transport protein; Region: TrkH; cl10514 688245012481 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 688245012482 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 688245012483 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012484 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012485 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; cl09110 688245012486 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 688245012487 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 688245012488 putative catalytic cysteine; other site 688245012489 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 688245012490 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 688245012491 Rare lipoprotein B family; Region: RplB; cl01125 688245012492 leucyl-tRNA synthetase, eubacterial and mitochondrial family; Region: leuS_bact; TIGR00396 688245012493 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 688245012494 HIGH motif; other site 688245012495 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 688245012496 KMSKS motif; other site 688245012497 active site 688245012498 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 688245012499 tRNA binding surface; other site 688245012500 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 688245012501 Mechanosensitive ion channel; Region: MS_channel; pfam00924 688245012502 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 688245012503 conserved cys residue; other site 688245012504 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 688245012505 META domain; Region: META; cl01245 688245012506 Nuclease-related domain; Region: NERD; pfam08378 688245012507 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 688245012508 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 688245012509 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 688245012510 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 688245012511 Walker A/P-loop; other site 688245012512 ATP binding site; other site 688245012513 Q-loop/lid; other site 688245012514 ABC transporter signature motif; other site 688245012515 Walker B; other site 688245012516 D-loop; other site 688245012517 H-loop/switch region; other site 688245012518 AIR carboxylase; Region: AIRC; cl00310 688245012519 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 688245012520 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245012521 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 688245012522 SUA5 domain; Region: SUA5; pfam03481 688245012523 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 688245012524 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 688245012525 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 688245012526 Walker A/P-loop; other site 688245012527 ATP binding site; other site 688245012528 Q-loop/lid; other site 688245012529 ABC transporter signature motif; other site 688245012530 Walker B; other site 688245012531 D-loop; other site 688245012532 H-loop/switch region; other site 688245012533 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...; Region: TM_PBP2; cd06261 688245012534 ABC-ATPase subunit interface; other site 688245012535 putative PBP binding loops; other site 688245012536 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245012537 active site 688245012538 Surface antigen; Region: Surface_Ag_2; cl01155 688245012539 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 688245012540 active site 688245012541 catalytic triad; other site 688245012542 oxyanion hole; other site 688245012543 Beta-lactamase; Region: Beta-lactamase; cl01009 688245012544 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 688245012545 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 688245012546 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 688245012547 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 688245012548 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 688245012549 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 688245012550 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 688245012551 dimer interface; other site 688245012552 NADP binding site; other site 688245012553 catalytic residues; other site 688245012554 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 688245012555 Transcriptional regulators [Transcription]; Region: GntR; COG1802 688245012556 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 688245012557 DNA binding site 688245012558 FCD domain; Region: FCD; cl11656 688245012559 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 688245012560 DctM-like transporters; Region: DctM; pfam06808 688245012561 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; cl09110 688245012562 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 688245012563 potential frameshift: common BLAST hit: gi|115360848|ref|YP_777985.1| dihydrodipicolinate synthetase 688245012564 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 688245012565 inhibitor site; inhibition site 688245012566 active site 688245012567 dimer interface; other site 688245012568 catalytic residue; other site 688245012569 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 688245012570 Major Facilitator Superfamily; Region: MFS_1; pfam07690 688245012571 putative substrate translocation pore; other site 688245012572 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...; Region: gram_neg_porins; cd00342 688245012573 trimer interface; other site 688245012574 eyelet of channel; other site 688245012575 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 688245012576 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...; Region: PDR_like; cd06185 688245012577 FMN-binding pocket; other site 688245012578 flavin binding motif; other site 688245012579 phosphate binding motif; other site 688245012580 beta-alpha-beta structure motif; other site 688245012581 NAD binding pocket; other site 688245012582 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 688245012583 catalytic loop; other site 688245012584 iron binding site; other site 688245012585 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 688245012586 homotrimer interaction site; other site 688245012587 putative active site; other site 688245012588 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 688245012589 [2Fe-2S] cluster binding site; other site 688245012590 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 688245012591 hydrophobic ligand binding site; other site 688245012592 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 688245012593 Predicted ring-cleavage extradiol dioxygenase [General function prediction only]; Region: COG2514 688245012594 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 688245012595 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 688245012596 NAD(P) binding site; other site 688245012597 catalytic residues; other site 688245012598 hypothetical protein; Provisional; Region: PRK07064 688245012599 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 688245012600 PYR/PP interface; other site 688245012601 dimer interface; other site 688245012602 TPP binding site; other site 688245012603 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 688245012604 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...; Region: TPP_enzymes; cd00568 688245012605 TPP-binding site; other site 688245012606 short chain dehydrogenase; Provisional; Region: PRK07062 688245012607 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 688245012608 putative NAD(P) binding site; other site 688245012609 putative active site; other site 688245012610 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012611 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245012612 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245012613 short chain dehydrogenase; Provisional; Region: PRK12939 688245012614 classical (c) SDRs; Region: SDR_c; cd05233 688245012615 NAD(P) binding site; other site 688245012616 active site 688245012617 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 688245012618 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 688245012619 L-aspartate dehydrogenase; Provisional; Region: PRK13303 688245012620 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012621 Domain of unknown function DUF108; Region: DUF108; pfam01958 688245012622 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012623 Transcriptional regulator [Transcription]; Region: IclR; COG1414 688245012624 Bacterial transcriptional regulator; Region: IclR; pfam01614 688245012625 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 688245012626 Cupin domain; Region: Cupin_2; cl09118 688245012627 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 688245012628 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245012629 hypothetical protein; Provisional; Region: PRK08185 688245012630 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...; Region: TBP_aldolase_IIB; cd00947 688245012631 intersubunit interface; other site 688245012632 active site 688245012633 zinc binding site; other site 688245012634 Na+ binding site; other site 688245012635 sensor protein QseC; Provisional; Region: PRK10337 688245012636 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 trans-...; Region: HisKA; cd00082 688245012637 dimer interface; other site 688245012638 phosphorylation site 688245012639 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 688245012640 ATP binding site; other site 688245012641 Mg2+ binding site; other site 688245012642 G-X-G motif; other site 688245012643 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 688245012644 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 688245012645 active site 688245012646 phosphorylation site 688245012647 intermolecular recognition site; other site 688245012648 dimerization interface; other site 688245012649 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...; Region: trans_reg_C; cd00383 688245012650 DNA binding site 688245012651 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 688245012652 active site 688245012653 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 688245012654 active site 688245012655 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 688245012656 active site 688245012657 pyruvate kinase; Provisional; Region: PRK05826 688245012658 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; cl10032 688245012659 domain interfaces; other site 688245012660 active site 688245012661 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 688245012662 proline aminopeptidase P II; Provisional; Region: PRK10879 688245012663 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...; Region: Prolidase; cd01087 688245012664 active site 688245012665 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 688245012666 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 688245012667 Substrate binding site; other site 688245012668 metal-binding site 688245012669 transketolase; Reviewed; Region: PRK12753 688245012670 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 688245012671 TPP-binding site; other site 688245012672 dimer interface; other site 688245012673 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 688245012674 PYR/PP interface; other site 688245012675 dimer interface; other site 688245012676 TPP binding site; other site 688245012677 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 688245012678 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 688245012679 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012680 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 688245012681 Rhomboid family; Region: Rhomboid; cl11446 688245012682 OsmC-like protein; Region: OsmC; cl00767 688245012683 Pirin-related protein [General function prediction only]; Region: COG1741 688245012684 Cupin domain; Region: Cupin_2; cl09118 688245012685 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 688245012686 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 688245012687 Aspartase; Region: Aspartase; cd01357 688245012688 active sites 688245012689 tetramer interface; other site 688245012690 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 688245012691 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 688245012692 dihydrodipicolinate reductase; Provisional; Region: PRK00048 688245012693 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012694 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 688245012695 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 688245012696 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 688245012697 metal binding site 2; metal-binding site 688245012698 putative DNA binding helix; other site 688245012699 metal binding site 1; metal-binding site 688245012700 dimer interface; other site 688245012701 structural Zn2+ binding site; other site 688245012702 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 688245012703 Protein of unknown function (DUF1501); Region: DUF1501; cl01699 688245012704 HPr kinase/phosphorylase; Provisional; Region: PRK05428 688245012705 DRTGG domain; Region: DRTGG; cl12147 688245012706 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-...; Region: HprK_C; cd01918 688245012707 Hpr binding site; other site 688245012708 active site 688245012709 homohexamer subunit interaction site; other site 688245012710 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 688245012711 active site 688245012712 phosphorylation site 688245012713 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 A site...; Region: RaiA; cd00552 688245012714 30S subunit binding site; other site 688245012715 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 688245012716 ATP binding site; other site 688245012717 active site 688245012718 substrate binding site; other site 688245012719 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 688245012720 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 688245012721 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 688245012722 transcriptional regulator; Provisional; Region: PRK10632 688245012723 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012724 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 688245012725 putative effector binding pocket; other site 688245012726 dimerization interface; other site 688245012727 Pirin-related protein [General function prediction only]; Region: COG1741 688245012728 Cupin domain; Region: Cupin_2; cl09118 688245012729 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 688245012730 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 688245012731 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...; Region: GST_N_Ure2p_like; cd03048 688245012732 C-terminal domain interface; other site 688245012733 GSH binding site (G-site); other site 688245012734 dimer interface; other site 688245012735 GST_C 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...; Region: GST_C_Ure2p_like; cd03178 688245012736 dimer interface; other site 688245012737 N-terminal domain interface; other site 688245012738 putative substrate binding pocket (H-site); other site 688245012739 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 688245012740 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 688245012741 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012742 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 688245012743 dimerization interface; other site 688245012744 substrate binding pocket; other site 688245012745 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 688245012746 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 688245012747 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 688245012748 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...; Region: PBPb; cd00134 688245012749 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 688245012750 substrate binding pocket; other site 688245012751 membrane-bound complex binding site; other site 688245012752 hinge residues; other site 688245012753 DTW domain; Region: DTW; cl01221 688245012754 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 688245012755 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 688245012756 S-adenosylmethionine binding site; other site 688245012757 DNA polymerase II large subunit; Provisional; Region: PRK14714 688245012758 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 688245012759 Flavin Reductases; Region: FlaRed; cl00801 688245012760 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 688245012761 PAS fold; Region: PAS_3; pfam08447 688245012762 putative active site; other site 688245012763 heme pocket; other site 688245012764 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 688245012765 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 688245012766 ATP binding site; other site 688245012767 Mg2+ binding site; other site 688245012768 G-X-G motif; other site 688245012769 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR7; cd08276 688245012770 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 688245012771 putative NAD(P) binding site; other site 688245012772 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012773 Isochorismatase family; Region: Isochorismatase; pfam00857 688245012774 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 688245012775 catalytic triad; other site 688245012776 dimer interface; other site 688245012777 conserved cis-peptide bond; other site 688245012778 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 688245012779 Isochorismatase family; Region: Isochorismatase; pfam00857 688245012780 catalytic triad; other site 688245012781 dimer interface; other site 688245012782 conserved cis-peptide bond; other site 688245012783 Pirin-related protein [General function prediction only]; Region: COG1741 688245012784 Cupin domain; Region: Cupin_2; cl09118 688245012785 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 688245012786 LysR family transcriptional regulator; Provisional; Region: PRK14997 688245012787 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012788 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 688245012789 putative effector binding pocket; other site 688245012790 putative dimerization interface; other site 688245012791 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...; Region: GSH_Peroxidase; cd00340 688245012792 catalytic residues; other site 688245012793 dimer interface; other site 688245012794 Transglycosylase; Region: Transgly; cl07896 688245012795 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 688245012796 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 688245012797 Sodium:solute symporter family; Region: SSF; cl00456 688245012798 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...; Region: RNase_Sa; cd00607 688245012799 active site 688245012800 barstar interaction site; other site 688245012801 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 688245012802 putative RNAase interaction site; other site 688245012803 Integral membrane protein TerC family; Region: TerC; cl10468 688245012804 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 688245012805 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 688245012806 active site 688245012807 phosphorylation site 688245012808 intermolecular recognition site; other site 688245012809 dimerization interface; other site 688245012810 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...; Region: LuxR_C_like; cd06170 688245012811 DNA binding residues 688245012812 dimerization interface; other site 688245012813 Histidine kinase; Region: HisKA_3; pfam07730 688245012814 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 688245012815 ATP binding site; other site 688245012816 Mg2+ binding site; other site 688245012817 G-X-G motif; other site 688245012818 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 688245012819 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 688245012820 Ligand Binding Site; other site 688245012821 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 688245012822 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012823 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 688245012824 putative dimerization interface; other site 688245012825 gluconate transporter; Region: gntP; TIGR00791 688245012826 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; cl09110 688245012827 tricarballylate dehydrogenase; Validated; Region: PRK08274 688245012828 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245012829 tricarballylate utilization protein B; Provisional; Region: PRK15033 688245012830 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 688245012831 Uncharacterized conserved protein [Function unknown]; Region: COG2128 688245012832 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 688245012833 RNA polymerase sigma factor SigJ; Provisional; Region: PRK09636 688245012834 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 688245012835 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...; Region: Sigma70_r4; cl01055 688245012836 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 688245012837 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 688245012838 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 688245012839 Transcriptional regulator [Transcription]; Region: LysR; COG0583 688245012840 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012841 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 688245012842 dimerization interface; other site 688245012843 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 688245012844 EamA-like transporter family; Region: EamA; cl01037 688245012845 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...; Region: Nudix_Hydrolase_2; cd03675 688245012846 nudix motif; other site 688245012847 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 688245012848 Coenzyme A binding pocket; other site 688245012849 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 688245012850 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 688245012851 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 688245012852 inhibitor-cofactor binding pocket; inhibition site 688245012853 pyridoxal 5'-phosphate binding site; other site 688245012854 catalytic residue; other site 688245012855 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; cl12011 688245012856 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 688245012857 SurA N-terminal domain; Region: SurA_N; pfam09312 688245012858 PPIC-type PPIASE domain; Region: Rotamase; cl08278 688245012859 PPIC-type PPIASE domain; Region: Rotamase; cl08278 688245012860 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 688245012861 OstA-like protein; Region: OstA; cl00844 688245012862 Organic solvent tolerance protein; Region: OstA_C; pfam04453 688245012863 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 688245012864 Phosphotransferase enzyme family; Region: APH; pfam01636 688245012865 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 688245012866 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 688245012867 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 688245012868 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; cl12031 688245012869 Peptidase dimerization domain; Region: M20_dimer; cl09126 688245012870 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 688245012871 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 688245012872 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 688245012873 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 688245012874 S-adenosylmethionine binding site; other site 688245012875 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; cl12031 688245012876 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 688245012877 Predicted membrane protein [Function unknown]; Region: COG2119 688245012878 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 688245012879 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 688245012880 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 688245012881 RNA/DNA binding site; other site 688245012882 RRM dimerization site; other site 688245012883 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 688245012884 RNA/DNA binding site; other site 688245012885 RRM dimerization site; other site 688245012886 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 688245012887 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245012888 NAD(P) binding site; other site 688245012889 active site 688245012890 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 688245012891 Protein of unknown function (DUF1239); Region: DUF1239; pfam06835 688245012892 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; cl11391 688245012893 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 688245012894 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 5-...; Region: SIS_Kpsf; cd05014 688245012895 putative active site; other site 688245012896 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 688245012897 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 688245012898 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 688245012899 ligand binding site; other site 688245012900 flexible hinge region; other site 688245012901 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 688245012902 substrate binding site; other site 688245012903 hinge regions; other site 688245012904 ADP binding site; other site 688245012905 catalytic site; other site 688245012906 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 688245012907 AzlC protein; Region: AzlC; cl00570 688245012908 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 688245012909 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 688245012910 putative active site; other site 688245012911 substrate binding site; other site 688245012912 putative cosubstrate binding site; other site 688245012913 catalytic site; other site 688245012914 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 688245012915 substrate binding site; other site 688245012916 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...; Region: Pep_deformylase; cd00487 688245012917 active site 688245012918 catalytic residues; other site 688245012919 metal-binding site 688245012920 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 688245012921 putative peptidoglycan binding site; other site 688245012922 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 688245012923 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 688245012924 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 688245012925 Protein export membrane protein; Region: SecD_SecF; cl14618 688245012926 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 688245012927 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 688245012928 Protein export membrane protein; Region: SecD_SecF; cl14618 688245012929 Preprotein translocase subunit; Region: YajC; cl00806 688245012930 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 688245012931 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 688245012932 dimer interface; other site 688245012933 PYR/PP interface; other site 688245012934 TPP binding site; other site 688245012935 substrate binding site; other site 688245012936 TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the...; Region: TPP_IOR_alpha; cd02008 688245012937 TPP-binding site; other site 688245012938 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 688245012939 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 688245012940 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245012941 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 688245012942 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 688245012943 putative substrate translocation pore; other site 688245012944 MltA specific insert domain; Region: MltA; pfam03562 688245012945 3D domain; Region: 3D; cl01439 688245012946 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 688245012947 ligand binding site; other site 688245012948 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 688245012949 active site 688245012950 phosphorylation site 688245012951 intermolecular recognition site; other site 688245012952 dimerization interface; other site 688245012953 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...; Region: LuxR_C_like; cd06170 688245012954 DNA binding residues 688245012955 dimerization interface; other site 688245012956 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 688245012957 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 688245012958 putative active site; other site 688245012959 heme pocket; other site 688245012960 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 trans-...; Region: HisKA; cl00080 688245012961 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 688245012962 ATP binding site; other site 688245012963 Mg2+ binding site; other site 688245012964 G-X-G motif; other site 688245012965 Predicted amidohydrolase [General function prediction only]; Region: COG0388 688245012966 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 688245012967 putative active site; other site 688245012968 catalytic triad; other site 688245012969 dimer interface; other site 688245012970 conserved hypothetical protein TIGR02099; Region: TIGR02099 688245012971 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 688245012972 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 688245012973 metal binding triad; other site 688245012974 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 688245012975 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 688245012976 metal binding triad; other site 688245012977 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 688245012978 putative glutathione S-transferase; Provisional; Region: PRK10357 688245012979 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 688245012980 putative C-terminal domain interface; other site 688245012981 putative GSH binding site (G-site); other site 688245012982 putative dimer interface; other site 688245012983 GST_C family, unknown subfamily 6; 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_C_6; cd03205 688245012984 putative N-terminal domain interface; other site 688245012985 putative dimer interface; other site 688245012986 putative substrate binding pocket (H-site); other site 688245012987 adenylosuccinate lyase; Provisional; Region: PRK09285 688245012988 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 688245012989 tetramer interface; other site 688245012990 active site 688245012991 YaeQ protein; Region: YaeQ; cl01913 688245012992 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 688245012993 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 688245012994 Integral membrane protein TerC family; Region: TerC; cl10468 688245012995 Membrane protein of unknown function; Region: DUF360; cl00850 688245012996 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 688245012997 Peptidase family M48; Region: Peptidase_M48; cl12018 688245012998 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...; Region: MoaC_PE; cd01420 688245012999 trimer interface; other site 688245013000 dimer interface; other site 688245013001 putative active site; other site 688245013002 O-Antigen ligase; Region: Wzy_C; cl04850 688245013003 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 688245013004 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 688245013005 Pilin (bacterial filament); Region: Pilin; pfam00114 688245013006 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 688245013007 phosphopeptide binding site; other site 688245013008 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 688245013009 dimer interface; other site 688245013010 ssDNA binding site; other site 688245013011 tetramer (dimer of dimers) interface; other site 688245013012 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 688245013013 putative substrate translocation pore; other site 688245013014 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 688245013015 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245013016 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 688245013017 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 688245013018 FAD dependent oxidoreductase; Region: DAO; pfam01266 688245013019 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 688245013020 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 688245013021 cell density-dependent motility repressor; Provisional; Region: PRK10082 688245013022 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245013023 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 688245013024 dimerization interface; other site 688245013025 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 contains two...; Region: OMP_decarboxylase_like; cd04725 688245013026 active site 688245013027 dimer interface; other site 688245013028 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 688245013029 EamA-like transporter family; Region: EamA; cl01037 688245013030 EamA-like transporter family; Region: EamA; cl01037 688245013031 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 5,10-...; Region: DHFR; cl00161 688245013032 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 688245013033 CoenzymeA binding site; other site 688245013034 subunit interaction site; other site 688245013035 PHB binding site; other site 688245013036 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 688245013037 DNA binding residues 688245013038 Integral membrane protein TerC family; Region: TerC; cl10468 688245013039 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 688245013040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245013041 CoA-ligase; Region: Ligase_CoA; pfam00549 688245013042 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 688245013043 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 688245013044 CoA-ligase; Region: Ligase_CoA; pfam00549 688245013045 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 688245013046 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 688245013047 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 688245013048 d-galactonate transporter; Region: 2A0114; TIGR00893 688245013049 putative substrate translocation pore; other site 688245013050 aromatic amino acid exporter; Provisional; Region: PRK11689 688245013051 EamA-like transporter family; Region: EamA; cl01037 688245013052 RecX family; Region: RecX; cl00936 688245013053 recombinase A; Provisional; Region: recA; PRK09354 688245013054 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 688245013055 hexamer interface; other site 688245013056 Walker A motif; other site 688245013057 ATP binding site; other site 688245013058 Walker B motif; other site 688245013059 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 688245013060 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 688245013061 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 688245013062 active site 688245013063 phosphorylation site 688245013064 intermolecular recognition site; other site 688245013065 dimerization interface; other site 688245013066 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...; Region: trans_reg_C; cd00383 688245013067 DNA binding site 688245013068 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 688245013069 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 688245013070 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 trans-...; Region: HisKA; cd00082 688245013071 dimer interface; other site 688245013072 phosphorylation site 688245013073 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 688245013074 ATP binding site; other site 688245013075 Mg2+ binding site; other site 688245013076 G-X-G motif; other site 688245013077 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 688245013078 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 688245013079 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 688245013080 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 688245013081 SET domain; Region: SET; cl02566 688245013082 DNA topoisomerase III; Provisional; Region: PRK14724 688245013083 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:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 688245013084 active site 688245013085 putative interdomain interaction site; other site 688245013086 putative metal-binding site; other site 688245013087 putative nucleotide binding site; other site 688245013088 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...; Region: TOP1Ac; cd00186 688245013089 domain I; other site 688245013090 DNA binding groove 688245013091 phosphate binding site; other site 688245013092 domain II; other site 688245013093 domain III; other site 688245013094 nucleotide binding site; other site 688245013095 catalytic site; other site 688245013096 domain IV; other site 688245013097 SWIB/MDM2 domain; Region: SWIB; cl02489 688245013098 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 688245013099 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 688245013100 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 688245013101 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 688245013102 putative ligand binding site; other site 688245013103 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 688245013104 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 688245013105 active site 688245013106 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 688245013107 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 688245013108 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 688245013109 malic enzyme; Reviewed; Region: PRK12862 688245013110 Malic enzyme, N-terminal domain; Region: malic; pfam00390 688245013111 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 688245013112 putative NAD(P) binding site; other site 688245013113 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 688245013114 Sulfatase; Region: Sulfatase; cl10460 688245013115 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 688245013116 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 688245013117 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 688245013118 G1 box; other site 688245013119 GTP/Mg2+ binding site; other site 688245013120 Switch I region; other site 688245013121 G2 box; other site 688245013122 Switch II region; other site 688245013123 G3 box; other site 688245013124 G4 box; other site 688245013125 G5 box; other site 688245013126 Uncharacterized conserved protein [Function unknown]; Region: COG4127 688245013127 Restriction endonuclease; Region: Mrr_cat; cl00747 688245013128 membrane protein insertase; Provisional; Region: PRK01318 688245013129 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 688245013130 Domain of unknown function DUF37; Region: DUF37; cl00506 688245013131 Ribonuclease P; Region: Ribonuclease_P; cl00457 688245013132 Ribosomal protein L34; Region: Ribosomal_L34; cl00370