-- dump date 20140620_032401 -- class Genbank::misc_feature -- table misc_feature_note -- id note 316055000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 316055000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 316055000003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055000004 Walker A motif; other site 316055000005 ATP binding site [chemical binding]; other site 316055000006 Walker B motif; other site 316055000007 arginine finger; other site 316055000008 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 316055000009 DnaA box-binding interface [nucleotide binding]; other site 316055000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 316055000011 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 316055000012 putative DNA binding surface [nucleotide binding]; other site 316055000013 dimer interface [polypeptide binding]; other site 316055000014 beta-clamp/clamp loader binding surface; other site 316055000015 beta-clamp/translesion DNA polymerase binding surface; other site 316055000016 recombination protein F; Reviewed; Region: recF; PRK00064 316055000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055000018 Walker A/P-loop; other site 316055000019 ATP binding site [chemical binding]; other site 316055000020 Q-loop/lid; other site 316055000021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055000022 ABC transporter signature motif; other site 316055000023 Walker B; other site 316055000024 D-loop; other site 316055000025 H-loop/switch region; other site 316055000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 316055000027 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 316055000028 Mg2+ binding site [ion binding]; other site 316055000029 G-X-G motif; other site 316055000030 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 316055000031 anchoring element; other site 316055000032 dimer interface [polypeptide binding]; other site 316055000033 ATP binding site [chemical binding]; other site 316055000034 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 316055000035 active site 316055000036 putative metal-binding site [ion binding]; other site 316055000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 316055000038 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055000039 HWE histidine kinase; Region: HWE_HK; smart00911 316055000040 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 316055000041 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 316055000042 putative DNA binding site [nucleotide binding]; other site 316055000043 putative Zn2+ binding site [ion binding]; other site 316055000044 AsnC family; Region: AsnC_trans_reg; pfam01037 316055000045 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 316055000046 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 316055000047 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 316055000048 metal-binding site [ion binding] 316055000049 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316055000050 Soluble P-type ATPase [General function prediction only]; Region: COG4087 316055000051 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 316055000052 FixH; Region: FixH; pfam05751 316055000053 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 316055000054 4Fe-4S binding domain; Region: Fer4_5; pfam12801 316055000055 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 316055000056 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 316055000057 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 316055000058 Cytochrome c; Region: Cytochrom_C; pfam00034 316055000059 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 316055000060 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 316055000061 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 316055000062 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 316055000063 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 316055000064 Low-spin heme binding site [chemical binding]; other site 316055000065 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 316055000066 Putative water exit pathway; other site 316055000067 Binuclear center (active site) [active] 316055000068 Putative proton exit pathway; other site 316055000069 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 316055000070 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 316055000071 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 316055000072 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 316055000073 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 316055000074 putative NAD(P) binding site [chemical binding]; other site 316055000075 active site 316055000076 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 316055000077 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 316055000078 putative catalytic residue [active] 316055000079 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055000080 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 316055000081 putative C-terminal domain interface [polypeptide binding]; other site 316055000082 putative GSH binding site (G-site) [chemical binding]; other site 316055000083 putative dimer interface [polypeptide binding]; other site 316055000084 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 316055000085 putative N-terminal domain interface [polypeptide binding]; other site 316055000086 putative dimer interface [polypeptide binding]; other site 316055000087 putative substrate binding pocket (H-site) [chemical binding]; other site 316055000088 short chain dehydrogenase; Provisional; Region: PRK08278 316055000089 human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs; Region: HSDL2_SDR_c; cd09762 316055000090 NAD(P) binding site [chemical binding]; other site 316055000091 homodimer interface [polypeptide binding]; other site 316055000092 active site 316055000093 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 316055000094 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 316055000095 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 316055000096 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 316055000097 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 316055000098 purine monophosphate binding site [chemical binding]; other site 316055000099 dimer interface [polypeptide binding]; other site 316055000100 putative catalytic residues [active] 316055000101 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 316055000102 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 316055000103 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 316055000104 16S rRNA methyltransferase B; Provisional; Region: PRK10901 316055000105 NusB family; Region: NusB; pfam01029 316055000106 putative RNA binding site [nucleotide binding]; other site 316055000107 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 316055000108 S-adenosylmethionine binding site [chemical binding]; other site 316055000109 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 316055000110 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 316055000111 RES domain; Region: RES; smart00953 316055000112 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 316055000113 non-specific DNA binding site [nucleotide binding]; other site 316055000114 sequence-specific DNA binding site [nucleotide binding]; other site 316055000115 salt bridge; other site 316055000116 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 316055000117 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 316055000118 Catalytic site; other site 316055000119 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 316055000120 Alkaline phosphatase homologues; Region: alkPPc; smart00098 316055000121 active site 316055000122 dimer interface [polypeptide binding]; other site 316055000123 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 316055000124 argininosuccinate synthase; Validated; Region: PRK05370 316055000125 argininosuccinate synthase; Provisional; Region: PRK13820 316055000126 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 316055000127 active site 316055000128 HD domain; Region: HD_3; pfam13023 316055000129 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 316055000130 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 316055000131 FeS/SAM binding site; other site 316055000132 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 316055000133 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 316055000134 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 316055000135 NAD(P) binding site [chemical binding]; other site 316055000136 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 316055000137 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055000138 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055000139 Coenzyme A binding pocket [chemical binding]; other site 316055000140 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 316055000141 dimer interface [polypeptide binding]; other site 316055000142 substrate binding site [chemical binding]; other site 316055000143 metal binding sites [ion binding]; metal-binding site 316055000144 hypothetical protein; Provisional; Region: PRK08262 316055000145 M20 Peptidase, carboxypeptidase yscS; Region: M20_yscS; cd05674 316055000146 metal binding site [ion binding]; metal-binding site 316055000147 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 316055000148 HAMP domain; Region: HAMP; pfam00672 316055000149 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055000150 dimer interface [polypeptide binding]; other site 316055000151 putative CheW interface [polypeptide binding]; other site 316055000152 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 316055000153 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 316055000154 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 316055000155 homodimer interface [polypeptide binding]; other site 316055000156 NADP binding site [chemical binding]; other site 316055000157 substrate binding site [chemical binding]; other site 316055000158 hypothetical protein; Validated; Region: PRK01310 316055000159 YGGT family; Region: YGGT; pfam02325 316055000160 SnoaL-like domain; Region: SnoaL_2; pfam12680 316055000161 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 316055000162 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 316055000163 catalytic triad [active] 316055000164 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 316055000165 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055000166 NAD(P) binding site [chemical binding]; other site 316055000167 active site 316055000168 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 316055000169 putative metal binding site [ion binding]; other site 316055000170 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055000171 cyclase homology domain; Region: CHD; cd07302 316055000172 nucleotidyl binding site; other site 316055000173 metal binding site [ion binding]; metal-binding site 316055000174 dimer interface [polypeptide binding]; other site 316055000175 Cytochrome P450; Region: p450; cl12078 316055000176 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 316055000177 Transmembrane secretion effector; Region: MFS_3; pfam05977 316055000178 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 316055000179 putative substrate translocation pore; other site 316055000180 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 316055000181 Part of AAA domain; Region: AAA_19; pfam13245 316055000182 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 316055000183 AAA domain; Region: AAA_12; pfam13087 316055000184 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 316055000185 putative active site [active] 316055000186 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 316055000187 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 316055000188 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 316055000189 HemY protein N-terminus; Region: HemY_N; pfam07219 316055000190 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 316055000191 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 316055000192 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 316055000193 active site 316055000194 UGMP family protein; Validated; Region: PRK09604 316055000195 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 316055000196 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 316055000197 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 316055000198 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 316055000199 EVE domain; Region: EVE; pfam01878 316055000200 Predicted methyltransferase [General function prediction only]; Region: COG3897 316055000201 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055000202 acetyl-CoA synthetase; Provisional; Region: PRK00174 316055000203 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 316055000204 active site 316055000205 CoA binding site [chemical binding]; other site 316055000206 acyl-activating enzyme (AAE) consensus motif; other site 316055000207 AMP binding site [chemical binding]; other site 316055000208 acetate binding site [chemical binding]; other site 316055000209 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 316055000210 S-adenosylmethionine binding site [chemical binding]; other site 316055000211 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 316055000212 CoenzymeA binding site [chemical binding]; other site 316055000213 subunit interaction site [polypeptide binding]; other site 316055000214 PHB binding site; other site 316055000215 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 316055000216 CoenzymeA binding site [chemical binding]; other site 316055000217 subunit interaction site [polypeptide binding]; other site 316055000218 PHB binding site; other site 316055000219 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055000220 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055000221 active site 316055000222 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 316055000223 substrate binding site [chemical binding]; other site 316055000224 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 316055000225 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 316055000226 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_4; pfam13661 316055000227 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 316055000228 Cytochrome P450; Region: p450; cl12078 316055000229 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055000230 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 316055000231 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 316055000232 Catalytic site; other site 316055000233 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055000234 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 316055000235 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055000236 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 316055000237 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 316055000238 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 316055000239 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055000240 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 316055000241 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055000242 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 316055000243 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 316055000244 PAS domain; Region: PAS; smart00091 316055000245 PAS fold; Region: PAS_7; pfam12860 316055000246 PAS domain S-box; Region: sensory_box; TIGR00229 316055000247 PAS domain; Region: PAS; smart00091 316055000248 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055000249 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055000250 metal binding site [ion binding]; metal-binding site 316055000251 active site 316055000252 I-site; other site 316055000253 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 316055000254 penicillin-insensitive murein endopeptidase; Reviewed; Region: mepA; PRK09429 316055000255 potassium/proton antiporter; Reviewed; Region: PRK05326 316055000256 Transporter associated domain; Region: CorC_HlyC; smart01091 316055000257 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 316055000258 active site 316055000259 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 316055000260 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 316055000261 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 316055000262 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 316055000263 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 316055000264 Methyltransferase domain; Region: Methyltransf_11; pfam08241 316055000265 Ku-homolog [Replication, recombination, and repair]; Region: COG1273 316055000266 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 316055000267 putative DNA binding site [nucleotide binding]; other site 316055000268 putative homodimer interface [polypeptide binding]; other site 316055000269 hypothetical protein; Reviewed; Region: PRK00024 316055000270 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 316055000271 MPN+ (JAMM) motif; other site 316055000272 Zinc-binding site [ion binding]; other site 316055000273 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 316055000274 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 316055000275 putative ligand binding site [chemical binding]; other site 316055000276 NAD binding site [chemical binding]; other site 316055000277 catalytic site [active] 316055000278 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055000279 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 316055000280 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 316055000281 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055000282 Walker A/P-loop; other site 316055000283 ATP binding site [chemical binding]; other site 316055000284 Q-loop/lid; other site 316055000285 ABC transporter signature motif; other site 316055000286 Walker B; other site 316055000287 D-loop; other site 316055000288 H-loop/switch region; other site 316055000289 NMT1/THI5 like; Region: NMT1; pfam09084 316055000290 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 316055000291 Creatinine amidohydrolase; Region: Creatininase; pfam02633 316055000292 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 316055000293 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 316055000294 active site 316055000295 FMN binding site [chemical binding]; other site 316055000296 substrate binding site [chemical binding]; other site 316055000297 3Fe-4S cluster binding site [ion binding]; other site 316055000298 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055000299 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 316055000300 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316055000301 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 316055000302 Prostaglandin dehydrogenases; Region: PGDH; cd05288 316055000303 NAD(P) binding site [chemical binding]; other site 316055000304 substrate binding site [chemical binding]; other site 316055000305 dimer interface [polypeptide binding]; other site 316055000306 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 316055000307 binding surface 316055000308 TPR motif; other site 316055000309 Tetratricopeptide repeat; Region: TPR_16; pfam13432 316055000310 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 316055000311 TPR motif; other site 316055000312 binding surface 316055000313 TPR repeat; Region: TPR_11; pfam13414 316055000314 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 316055000315 binding surface 316055000316 TPR motif; other site 316055000317 TPR repeat; Region: TPR_11; pfam13414 316055000318 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 316055000319 binding surface 316055000320 TPR motif; other site 316055000321 Tetratricopeptide repeat; Region: TPR_12; pfam13424 316055000322 Tetratricopeptide repeat; Region: TPR_12; pfam13424 316055000323 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 316055000324 binding surface 316055000325 TPR motif; other site 316055000326 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 316055000327 S-adenosylmethionine binding site [chemical binding]; other site 316055000328 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 316055000329 Predicted membrane protein [Function unknown]; Region: COG2261 316055000330 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 316055000331 classical (c) SDRs; Region: SDR_c; cd05233 316055000332 NAD(P) binding site [chemical binding]; other site 316055000333 active site 316055000334 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055000335 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055000336 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055000337 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055000338 active site 316055000339 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 316055000340 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 316055000341 substrate binding site [chemical binding]; other site 316055000342 oxyanion hole (OAH) forming residues; other site 316055000343 trimer interface [polypeptide binding]; other site 316055000344 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 316055000345 Peptidase family M48; Region: Peptidase_M48; pfam01435 316055000346 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 316055000347 Ferredoxin [Energy production and conversion]; Region: COG1146 316055000348 4Fe-4S binding domain; Region: Fer4; pfam00037 316055000349 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 316055000350 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 316055000351 RNA binding surface [nucleotide binding]; other site 316055000352 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 316055000353 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 316055000354 ATP binding site [chemical binding]; other site 316055000355 putative Mg++ binding site [ion binding]; other site 316055000356 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 316055000357 nucleotide binding region [chemical binding]; other site 316055000358 ATP-binding site [chemical binding]; other site 316055000359 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 316055000360 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 316055000361 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 316055000362 dimerization interface [polypeptide binding]; other site 316055000363 PAS domain; Region: PAS_9; pfam13426 316055000364 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 316055000365 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 316055000366 putative active site [active] 316055000367 heme pocket [chemical binding]; other site 316055000368 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055000369 dimer interface [polypeptide binding]; other site 316055000370 phosphorylation site [posttranslational modification] 316055000371 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 316055000372 ATP binding site [chemical binding]; other site 316055000373 G-X-G motif; other site 316055000374 Response regulator receiver domain; Region: Response_reg; pfam00072 316055000375 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 316055000376 active site 316055000377 phosphorylation site [posttranslational modification] 316055000378 intermolecular recognition site; other site 316055000379 dimerization interface [polypeptide binding]; other site 316055000380 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 316055000381 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 316055000382 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 316055000383 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 316055000384 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 316055000385 metal ion-dependent adhesion site (MIDAS); other site 316055000386 Domain of unknown function DUF29; Region: DUF29; pfam01724 316055000387 Domain of unknown function DUF29; Region: DUF29; pfam01724 316055000388 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 316055000389 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 316055000390 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 316055000391 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 316055000392 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 316055000393 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 316055000394 HSP70 interaction site [polypeptide binding]; other site 316055000395 BolA-like protein; Region: BolA; pfam01722 316055000396 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 316055000397 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 316055000398 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 316055000399 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 316055000400 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 316055000401 active site 316055000402 DNA binding site [nucleotide binding] 316055000403 Int/Topo IB signature motif; other site 316055000404 shikimate kinase; Provisional; Region: PRK13946 316055000405 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 316055000406 ADP binding site [chemical binding]; other site 316055000407 magnesium binding site [ion binding]; other site 316055000408 putative shikimate binding site; other site 316055000409 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 316055000410 active site 316055000411 dimer interface [polypeptide binding]; other site 316055000412 metal binding site [ion binding]; metal-binding site 316055000413 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 316055000414 Domain of unknown function DUF21; Region: DUF21; pfam01595 316055000415 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 316055000416 Transporter associated domain; Region: CorC_HlyC; smart01091 316055000417 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 316055000418 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 316055000419 SEC-C motif; Region: SEC-C; pfam02810 316055000420 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 316055000421 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 316055000422 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 316055000423 heterotetramer interface [polypeptide binding]; other site 316055000424 active site pocket [active] 316055000425 cleavage site 316055000426 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 316055000427 active site 316055000428 8-oxo-dGMP binding site [chemical binding]; other site 316055000429 nudix motif; other site 316055000430 metal binding site [ion binding]; metal-binding site 316055000431 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 316055000432 Methyltransferase domain; Region: Methyltransf_11; pfam08241 316055000433 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 316055000434 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055000435 active site 316055000436 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 316055000437 GSH binding site [chemical binding]; other site 316055000438 catalytic residues [active] 316055000439 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 316055000440 nitrilase; Region: PLN02798 316055000441 putative active site [active] 316055000442 catalytic triad [active] 316055000443 dimer interface [polypeptide binding]; other site 316055000444 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 316055000445 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 316055000446 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 316055000447 S-adenosylmethionine binding site [chemical binding]; other site 316055000448 aspartate kinase; Reviewed; Region: PRK06635 316055000449 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 316055000450 putative nucleotide binding site [chemical binding]; other site 316055000451 putative catalytic residues [active] 316055000452 putative Mg ion binding site [ion binding]; other site 316055000453 putative aspartate binding site [chemical binding]; other site 316055000454 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 316055000455 putative allosteric regulatory site; other site 316055000456 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 316055000457 putative allosteric regulatory residue; other site 316055000458 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 316055000459 GAF domain; Region: GAF; pfam01590 316055000460 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 316055000461 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 316055000462 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 316055000463 peptide chain release factor 1; Validated; Region: prfA; PRK00591 316055000464 This domain is found in peptide chain release factors; Region: PCRF; smart00937 316055000465 RF-1 domain; Region: RF-1; pfam00472 316055000466 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 316055000467 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 316055000468 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 316055000469 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055000470 Methyltransferase domain; Region: Methyltransf_11; pfam08241 316055000471 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316055000472 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 316055000473 EamA-like transporter family; Region: EamA; pfam00892 316055000474 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 316055000475 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 316055000476 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 316055000477 NAD(P) binding site [chemical binding]; other site 316055000478 homotetramer interface [polypeptide binding]; other site 316055000479 homodimer interface [polypeptide binding]; other site 316055000480 active site 316055000481 putative acyltransferase; Provisional; Region: PRK05790 316055000482 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 316055000483 dimer interface [polypeptide binding]; other site 316055000484 active site 316055000485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 316055000486 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 316055000487 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 316055000488 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055000489 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055000490 metal binding site [ion binding]; metal-binding site 316055000491 active site 316055000492 I-site; other site 316055000493 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 316055000494 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 316055000495 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 316055000496 Transglycosylase; Region: Transgly; cl17702 316055000497 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 316055000498 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 316055000499 substrate binding pocket [chemical binding]; other site 316055000500 chain length determination region; other site 316055000501 substrate-Mg2+ binding site; other site 316055000502 catalytic residues [active] 316055000503 aspartate-rich region 1; other site 316055000504 active site lid residues [active] 316055000505 aspartate-rich region 2; other site 316055000506 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 316055000507 Sensors of blue-light using FAD; Region: BLUF; pfam04940 316055000508 PAS fold; Region: PAS_7; pfam12860 316055000509 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055000510 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055000511 metal binding site [ion binding]; metal-binding site 316055000512 active site 316055000513 I-site; other site 316055000514 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 316055000515 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 316055000516 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 316055000517 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 316055000518 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 316055000519 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 316055000520 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 316055000521 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 316055000522 EamA-like transporter family; Region: EamA; pfam00892 316055000523 EamA-like transporter family; Region: EamA; pfam00892 316055000524 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316055000525 metal binding site 2 [ion binding]; metal-binding site 316055000526 putative DNA binding helix; other site 316055000527 metal binding site 1 [ion binding]; metal-binding site 316055000528 dimer interface [polypeptide binding]; other site 316055000529 structural Zn2+ binding site [ion binding]; other site 316055000530 MarR family; Region: MarR; pfam01047 316055000531 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 316055000532 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055000533 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055000534 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 316055000535 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 316055000536 putative substrate translocation pore; other site 316055000537 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 316055000538 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 316055000539 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 316055000540 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 316055000541 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 316055000542 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 316055000543 RNase E interface [polypeptide binding]; other site 316055000544 trimer interface [polypeptide binding]; other site 316055000545 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 316055000546 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 316055000547 RNase E interface [polypeptide binding]; other site 316055000548 trimer interface [polypeptide binding]; other site 316055000549 active site 316055000550 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 316055000551 putative nucleic acid binding region [nucleotide binding]; other site 316055000552 G-X-X-G motif; other site 316055000553 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 316055000554 RNA binding site [nucleotide binding]; other site 316055000555 domain interface; other site 316055000556 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 316055000557 16S/18S rRNA binding site [nucleotide binding]; other site 316055000558 S13e-L30e interaction site [polypeptide binding]; other site 316055000559 25S rRNA binding site [nucleotide binding]; other site 316055000560 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 316055000561 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 316055000562 RNA binding site [nucleotide binding]; other site 316055000563 active site 316055000564 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 316055000565 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 316055000566 translation initiation factor IF-2; Region: IF-2; TIGR00487 316055000567 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 316055000568 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 316055000569 G1 box; other site 316055000570 putative GEF interaction site [polypeptide binding]; other site 316055000571 GTP/Mg2+ binding site [chemical binding]; other site 316055000572 Switch I region; other site 316055000573 G2 box; other site 316055000574 G3 box; other site 316055000575 Switch II region; other site 316055000576 G4 box; other site 316055000577 G5 box; other site 316055000578 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 316055000579 Translation-initiation factor 2; Region: IF-2; pfam11987 316055000580 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 316055000581 hypothetical protein; Provisional; Region: PRK09190 316055000582 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 316055000583 putative RNA binding cleft [nucleotide binding]; other site 316055000584 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 316055000585 NusA N-terminal domain; Region: NusA_N; pfam08529 316055000586 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 316055000587 RNA binding site [nucleotide binding]; other site 316055000588 homodimer interface [polypeptide binding]; other site 316055000589 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 316055000590 G-X-X-G motif; other site 316055000591 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 316055000592 G-X-X-G motif; other site 316055000593 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 316055000594 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 316055000595 Sm and related proteins; Region: Sm_like; cl00259 316055000596 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 316055000597 putative oligomer interface [polypeptide binding]; other site 316055000598 putative RNA binding site [nucleotide binding]; other site 316055000599 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 316055000600 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055000601 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 316055000602 non-specific DNA binding site [nucleotide binding]; other site 316055000603 salt bridge; other site 316055000604 sequence-specific DNA binding site [nucleotide binding]; other site 316055000605 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 316055000606 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 316055000607 putative active site [active] 316055000608 catalytic triad [active] 316055000609 putative dimer interface [polypeptide binding]; other site 316055000610 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 316055000611 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 316055000612 Transporter associated domain; Region: CorC_HlyC; smart01091 316055000613 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG0319 316055000614 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 316055000615 PhoH-like protein; Region: PhoH; pfam02562 316055000616 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 316055000617 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 316055000618 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 316055000619 FeS/SAM binding site; other site 316055000620 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316055000621 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 316055000622 motif II; other site 316055000623 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316055000624 metal binding site 2 [ion binding]; metal-binding site 316055000625 putative DNA binding helix; other site 316055000626 metal binding site 1 [ion binding]; metal-binding site 316055000627 dimer interface [polypeptide binding]; other site 316055000628 structural Zn2+ binding site [ion binding]; other site 316055000629 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 316055000630 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055000631 Coenzyme A binding pocket [chemical binding]; other site 316055000632 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 316055000633 Glycoprotease family; Region: Peptidase_M22; pfam00814 316055000634 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 316055000635 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 316055000636 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 316055000637 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055000638 Walker A/P-loop; other site 316055000639 ATP binding site [chemical binding]; other site 316055000640 ABC transporter signature motif; other site 316055000641 Walker B; other site 316055000642 D-loop; other site 316055000643 H-loop/switch region; other site 316055000644 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055000645 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 316055000646 Ligand Binding Site [chemical binding]; other site 316055000647 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 316055000648 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 316055000649 active site 316055000650 HIGH motif; other site 316055000651 dimer interface [polypeptide binding]; other site 316055000652 KMSKS motif; other site 316055000653 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 316055000654 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 316055000655 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 316055000656 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 316055000657 substrate binding site [chemical binding]; other site 316055000658 ATP binding site [chemical binding]; other site 316055000659 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055000660 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055000661 succinic semialdehyde dehydrogenase; Region: PLN02278 316055000662 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 316055000663 tetramerization interface [polypeptide binding]; other site 316055000664 NAD(P) binding site [chemical binding]; other site 316055000665 catalytic residues [active] 316055000666 Predicted membrane protein [Function unknown]; Region: COG1971 316055000667 Domain of unknown function DUF; Region: DUF204; pfam02659 316055000668 Domain of unknown function DUF; Region: DUF204; pfam02659 316055000669 yybP-ykoY element as predicted by Rfam (RF00080) 316055000670 Transglycosylase; Region: Transgly; pfam00912 316055000671 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 316055000672 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 316055000673 Protein of unknown function DUF45; Region: DUF45; pfam01863 316055000674 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 316055000675 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 316055000676 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316055000677 ABC-2 type transporter; Region: ABC2_membrane; cl17235 316055000678 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 316055000679 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055000680 Walker A/P-loop; other site 316055000681 ATP binding site [chemical binding]; other site 316055000682 Q-loop/lid; other site 316055000683 ABC transporter signature motif; other site 316055000684 Walker B; other site 316055000685 D-loop; other site 316055000686 H-loop/switch region; other site 316055000687 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055000688 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055000689 dimer interface [polypeptide binding]; other site 316055000690 phosphorylation site [posttranslational modification] 316055000691 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 316055000692 ATP binding site [chemical binding]; other site 316055000693 Mg2+ binding site [ion binding]; other site 316055000694 G-X-G motif; other site 316055000695 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 316055000696 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 316055000697 active site 316055000698 phosphorylation site [posttranslational modification] 316055000699 intermolecular recognition site; other site 316055000700 dimerization interface [polypeptide binding]; other site 316055000701 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 316055000702 Protein of unknown function (DUF1052); Region: DUF1052; pfam06319 316055000703 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 316055000704 metal ion-dependent adhesion site (MIDAS); other site 316055000705 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 316055000706 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 316055000707 PAS fold; Region: PAS_3; pfam08447 316055000708 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 316055000709 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 316055000710 histidine kinase; Provisional; Region: PRK13557 316055000711 putative active site [active] 316055000712 heme pocket [chemical binding]; other site 316055000713 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055000714 dimer interface [polypeptide binding]; other site 316055000715 phosphorylation site [posttranslational modification] 316055000716 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 316055000717 ATP binding site [chemical binding]; other site 316055000718 Mg2+ binding site [ion binding]; other site 316055000719 G-X-G motif; other site 316055000720 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 316055000721 active site 316055000722 phosphorylation site [posttranslational modification] 316055000723 intermolecular recognition site; other site 316055000724 dimerization interface [polypeptide binding]; other site 316055000725 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 316055000726 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055000727 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 316055000728 Chromate transporter; Region: Chromate_transp; pfam02417 316055000729 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 316055000730 Predicted membrane protein [Function unknown]; Region: COG1289 316055000731 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 316055000732 PAS fold; Region: PAS_4; pfam08448 316055000733 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 316055000734 putative active site [active] 316055000735 heme pocket [chemical binding]; other site 316055000736 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055000737 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 316055000738 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 316055000739 ATP binding site [chemical binding]; other site 316055000740 substrate interface [chemical binding]; other site 316055000741 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 316055000742 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 316055000743 dimerization interface [polypeptide binding]; other site 316055000744 ligand binding site [chemical binding]; other site 316055000745 NADP binding site [chemical binding]; other site 316055000746 catalytic site [active] 316055000747 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 316055000748 Bacterial SH3 domain; Region: SH3_4; pfam06347 316055000749 Bacterial SH3 domain; Region: SH3_4; pfam06347 316055000750 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 316055000751 MutS domain I; Region: MutS_I; pfam01624 316055000752 MutS domain II; Region: MutS_II; pfam05188 316055000753 MutS domain III; Region: MutS_III; pfam05192 316055000754 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 316055000755 Walker A/P-loop; other site 316055000756 ATP binding site [chemical binding]; other site 316055000757 Q-loop/lid; other site 316055000758 ABC transporter signature motif; other site 316055000759 Walker B; other site 316055000760 D-loop; other site 316055000761 H-loop/switch region; other site 316055000762 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 316055000763 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 316055000764 dimer interface [polypeptide binding]; other site 316055000765 active site 316055000766 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 316055000767 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 316055000768 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 316055000769 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055000770 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316055000771 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 316055000772 Carboxylesterase family; Region: COesterase; pfam00135 316055000773 substrate binding pocket [chemical binding]; other site 316055000774 catalytic triad [active] 316055000775 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 316055000776 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055000777 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 316055000778 dimerization interface [polypeptide binding]; other site 316055000779 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 316055000780 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 316055000781 dimer interface [polypeptide binding]; other site 316055000782 active site 316055000783 heme binding site [chemical binding]; other site 316055000784 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 316055000785 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055000786 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 316055000787 putative C-terminal domain interface [polypeptide binding]; other site 316055000788 putative GSH binding site (G-site) [chemical binding]; other site 316055000789 putative dimer interface [polypeptide binding]; other site 316055000790 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 316055000791 dimer interface [polypeptide binding]; other site 316055000792 N-terminal domain interface [polypeptide binding]; other site 316055000793 putative substrate binding pocket (H-site) [chemical binding]; other site 316055000794 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06505 316055000795 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 316055000796 NAD binding site [chemical binding]; other site 316055000797 homotetramer interface [polypeptide binding]; other site 316055000798 homodimer interface [polypeptide binding]; other site 316055000799 substrate binding site [chemical binding]; other site 316055000800 active site 316055000801 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 316055000802 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 316055000803 dimer interface [polypeptide binding]; other site 316055000804 active site 316055000805 3-hydroxydecanoyl-(acyl carrier protein) dehydratase; Validated; Region: PRK05174 316055000806 active site 2 [active] 316055000807 active site 1 [active] 316055000808 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316055000809 metal binding site 2 [ion binding]; metal-binding site 316055000810 putative DNA binding helix; other site 316055000811 metal binding site 1 [ion binding]; metal-binding site 316055000812 dimer interface [polypeptide binding]; other site 316055000813 structural Zn2+ binding site [ion binding]; other site 316055000814 OsmC-like protein; Region: OsmC; pfam02566 316055000815 PII uridylyl-transferase; Provisional; Region: PRK05092 316055000816 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316055000817 metal binding triad; other site 316055000818 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316055000819 HD domain; Region: HD; pfam01966 316055000820 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 316055000821 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 316055000822 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 316055000823 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055000824 dimer interface [polypeptide binding]; other site 316055000825 phosphorylation site [posttranslational modification] 316055000826 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 316055000827 ATP binding site [chemical binding]; other site 316055000828 Mg2+ binding site [ion binding]; other site 316055000829 G-X-G motif; other site 316055000830 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 316055000831 active site 316055000832 phosphorylation site [posttranslational modification] 316055000833 intermolecular recognition site; other site 316055000834 dimerization interface [polypeptide binding]; other site 316055000835 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 316055000836 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 316055000837 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055000838 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055000839 putative ligand binding site [chemical binding]; other site 316055000840 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 316055000841 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 316055000842 putative catalytic cysteine [active] 316055000843 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 316055000844 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 316055000845 active site 316055000846 (T/H)XGH motif; other site 316055000847 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 316055000848 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 316055000849 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 316055000850 Peptidase family M23; Region: Peptidase_M23; pfam01551 316055000851 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 316055000852 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 316055000853 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 316055000854 protein binding site [polypeptide binding]; other site 316055000855 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 316055000856 Catalytic dyad [active] 316055000857 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 316055000858 putative active site [active] 316055000859 NodB motif; other site 316055000860 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 316055000861 putative active site [active] 316055000862 Ap4A binding site [chemical binding]; other site 316055000863 nudix motif; other site 316055000864 putative metal binding site [ion binding]; other site 316055000865 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 316055000866 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 316055000867 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055000868 NAD binding site [chemical binding]; other site 316055000869 putative substrate binding site 2 [chemical binding]; other site 316055000870 putative substrate binding site 1 [chemical binding]; other site 316055000871 active site 316055000872 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 316055000873 putative active site [active] 316055000874 Ap4A binding site [chemical binding]; other site 316055000875 nudix motif; other site 316055000876 putative metal binding site [ion binding]; other site 316055000877 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; cd00384 316055000878 dimer interface [polypeptide binding]; other site 316055000879 active site 316055000880 Schiff base residues; other site 316055000881 Cupin domain; Region: Cupin_2; cl17218 316055000882 Helix-turn-helix domain; Region: HTH_18; pfam12833 316055000883 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13448 316055000884 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 316055000885 gamma subunit interface [polypeptide binding]; other site 316055000886 epsilon subunit interface [polypeptide binding]; other site 316055000887 LBP interface [polypeptide binding]; other site 316055000888 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 316055000889 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 316055000890 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 316055000891 alpha subunit interaction interface [polypeptide binding]; other site 316055000892 Walker A motif; other site 316055000893 ATP binding site [chemical binding]; other site 316055000894 Walker B motif; other site 316055000895 inhibitor binding site; inhibition site 316055000896 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 316055000897 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 316055000898 core domain interface [polypeptide binding]; other site 316055000899 delta subunit interface [polypeptide binding]; other site 316055000900 epsilon subunit interface [polypeptide binding]; other site 316055000901 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 316055000902 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 316055000903 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 316055000904 beta subunit interaction interface [polypeptide binding]; other site 316055000905 Walker A motif; other site 316055000906 ATP binding site [chemical binding]; other site 316055000907 Walker B motif; other site 316055000908 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 316055000909 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 316055000910 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 316055000911 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 316055000912 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 316055000913 primosome assembly protein PriA; Validated; Region: PRK05580 316055000914 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 316055000915 ATP binding site [chemical binding]; other site 316055000916 putative Mg++ binding site [ion binding]; other site 316055000917 helicase superfamily c-terminal domain; Region: HELICc; smart00490 316055000918 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 316055000919 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 316055000920 active site 316055000921 DNA binding site [nucleotide binding] 316055000922 Int/Topo IB signature motif; other site 316055000923 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 316055000924 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 316055000925 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055000926 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055000927 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 316055000928 short chain dehydrogenase; Provisional; Region: PRK06123 316055000929 classical (c) SDRs; Region: SDR_c; cd05233 316055000930 NAD(P) binding site [chemical binding]; other site 316055000931 active site 316055000932 MAPEG family; Region: MAPEG; cl09190 316055000933 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 316055000934 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 316055000935 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 316055000936 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 316055000937 E3 interaction surface; other site 316055000938 lipoyl attachment site [posttranslational modification]; other site 316055000939 e3 binding domain; Region: E3_binding; pfam02817 316055000940 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 316055000941 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 316055000942 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 316055000943 TPP-binding site [chemical binding]; other site 316055000944 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 316055000945 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 316055000946 CoA binding domain; Region: CoA_binding; smart00881 316055000947 CoA-ligase; Region: Ligase_CoA; pfam00549 316055000948 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 316055000949 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 316055000950 CoA-ligase; Region: Ligase_CoA; pfam00549 316055000951 malate dehydrogenase; Reviewed; Region: PRK06223 316055000952 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 316055000953 NAD(P) binding site [chemical binding]; other site 316055000954 dimer interface [polypeptide binding]; other site 316055000955 tetramer (dimer of dimers) interface [polypeptide binding]; other site 316055000956 substrate binding site [chemical binding]; other site 316055000957 Predicted ATPase [General function prediction only]; Region: COG1485 316055000958 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 316055000959 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 316055000960 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 316055000961 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 316055000962 active site 316055000963 catalytic triad [active] 316055000964 oxyanion hole [active] 316055000965 switch loop; other site 316055000966 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055000967 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 316055000968 Walker A/P-loop; other site 316055000969 ATP binding site [chemical binding]; other site 316055000970 Q-loop/lid; other site 316055000971 ABC transporter signature motif; other site 316055000972 Walker B; other site 316055000973 D-loop; other site 316055000974 H-loop/switch region; other site 316055000975 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 316055000976 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 316055000977 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 316055000978 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 316055000979 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 316055000980 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 316055000981 Protein of unknown function (DUF1223); Region: DUF1223; pfam06764 316055000982 aconitate hydratase; Validated; Region: PRK09277 316055000983 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 316055000984 substrate binding site [chemical binding]; other site 316055000985 ligand binding site [chemical binding]; other site 316055000986 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 316055000987 substrate binding site [chemical binding]; other site 316055000988 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 316055000989 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055000990 Walker A/P-loop; other site 316055000991 ATP binding site [chemical binding]; other site 316055000992 Q-loop/lid; other site 316055000993 ABC transporter signature motif; other site 316055000994 Walker B; other site 316055000995 D-loop; other site 316055000996 H-loop/switch region; other site 316055000997 heme exporter protein CcmB; Region: ccmB; TIGR01190 316055000998 heme exporter protein CcmC; Region: ccmC; TIGR01191 316055000999 Heme exporter protein D (CcmD); Region: CcmD; cl11475 316055001000 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 316055001001 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 316055001002 catalytic residues [active] 316055001003 central insert; other site 316055001004 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 316055001005 intracellular septation protein A; Reviewed; Region: PRK00259 316055001006 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 316055001007 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 316055001008 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 316055001009 P loop; other site 316055001010 GTP binding site [chemical binding]; other site 316055001011 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 316055001012 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 316055001013 active site 316055001014 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 316055001015 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 316055001016 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 316055001017 FeS/SAM binding site; other site 316055001018 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 316055001019 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 316055001020 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 316055001021 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 316055001022 Uncharacterized conserved protein [Function unknown]; Region: COG2968 316055001023 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 316055001024 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 316055001025 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 316055001026 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001027 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001028 signal recognition particle protein; Provisional; Region: PRK10867 316055001029 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 316055001030 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 316055001031 P loop; other site 316055001032 GTP binding site [chemical binding]; other site 316055001033 Signal peptide binding domain; Region: SRP_SPB; pfam02978 316055001034 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 316055001035 RimM N-terminal domain; Region: RimM; pfam01782 316055001036 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 316055001037 PRC-barrel domain; Region: PRC; pfam05239 316055001038 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 316055001039 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 316055001040 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 316055001041 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 316055001042 substrate binding site [chemical binding]; other site 316055001043 ligand binding site [chemical binding]; other site 316055001044 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 316055001045 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 316055001046 CysD dimerization site [polypeptide binding]; other site 316055001047 G1 box; other site 316055001048 putative GEF interaction site [polypeptide binding]; other site 316055001049 GTP/Mg2+ binding site [chemical binding]; other site 316055001050 Switch I region; other site 316055001051 G2 box; other site 316055001052 G3 box; other site 316055001053 Switch II region; other site 316055001054 G4 box; other site 316055001055 G5 box; other site 316055001056 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 316055001057 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 316055001058 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 316055001059 ligand-binding site [chemical binding]; other site 316055001060 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 316055001061 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 316055001062 Active Sites [active] 316055001063 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein; Region: MMP_ACEL2062; cd12952 316055001064 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 316055001065 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 316055001066 substrate binding site [chemical binding]; other site 316055001067 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 316055001068 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 316055001069 active site clefts [active] 316055001070 zinc binding site [ion binding]; other site 316055001071 dimer interface [polypeptide binding]; other site 316055001072 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 316055001073 catalytic core [active] 316055001074 dihydrodipicolinate reductase; Provisional; Region: PRK00048 316055001075 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 316055001076 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 316055001077 Uncharacterized conserved protein [Function unknown]; Region: COG5470 316055001078 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 316055001079 active site 316055001080 dimer interface [polypeptide binding]; other site 316055001081 Predicted flavoprotein [General function prediction only]; Region: COG0431 316055001082 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 316055001083 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 316055001084 S-adenosylmethionine binding site [chemical binding]; other site 316055001085 chaperone protein DnaJ; Provisional; Region: PRK10767 316055001086 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 316055001087 HSP70 interaction site [polypeptide binding]; other site 316055001088 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 316055001089 substrate binding site [polypeptide binding]; other site 316055001090 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 316055001091 Zn binding sites [ion binding]; other site 316055001092 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 316055001093 dimer interface [polypeptide binding]; other site 316055001094 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 316055001095 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 316055001096 nucleotide binding site [chemical binding]; other site 316055001097 NEF interaction site [polypeptide binding]; other site 316055001098 SBD interface [polypeptide binding]; other site 316055001099 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 316055001100 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 316055001101 dimer interface [polypeptide binding]; other site 316055001102 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 316055001103 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 316055001104 ribonuclease PH; Reviewed; Region: rph; PRK00173 316055001105 Ribonuclease PH; Region: RNase_PH_bact; cd11362 316055001106 hexamer interface [polypeptide binding]; other site 316055001107 active site 316055001108 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 316055001109 active site 316055001110 dimerization interface [polypeptide binding]; other site 316055001111 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 316055001112 HemN C-terminal domain; Region: HemN_C; pfam06969 316055001113 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 316055001114 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055001115 putative ligand binding site [chemical binding]; other site 316055001116 Predicted methyltransferases [General function prediction only]; Region: COG0313 316055001117 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 316055001118 putative SAM binding site [chemical binding]; other site 316055001119 putative homodimer interface [polypeptide binding]; other site 316055001120 hypothetical protein; Reviewed; Region: PRK12497 316055001121 glutathione synthetase; Provisional; Region: PRK05246 316055001122 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 316055001123 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 316055001124 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 316055001125 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 316055001126 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 316055001127 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 316055001128 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 316055001129 PAS domain; Region: PAS_9; pfam13426 316055001130 putative active site [active] 316055001131 heme pocket [chemical binding]; other site 316055001132 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055001133 dimer interface [polypeptide binding]; other site 316055001134 phosphorylation site [posttranslational modification] 316055001135 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 316055001136 ATP binding site [chemical binding]; other site 316055001137 Mg2+ binding site [ion binding]; other site 316055001138 G-X-G motif; other site 316055001139 Response regulator receiver domain; Region: Response_reg; pfam00072 316055001140 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 316055001141 active site 316055001142 phosphorylation site [posttranslational modification] 316055001143 intermolecular recognition site; other site 316055001144 dimerization interface [polypeptide binding]; other site 316055001145 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 316055001146 pantothenate kinase; Provisional; Region: PRK05439 316055001147 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 316055001148 ATP-binding site [chemical binding]; other site 316055001149 CoA-binding site [chemical binding]; other site 316055001150 Mg2+-binding site [ion binding]; other site 316055001151 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 316055001152 metal binding site [ion binding]; metal-binding site 316055001153 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 316055001154 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 316055001155 substrate binding site [chemical binding]; other site 316055001156 glutamase interaction surface [polypeptide binding]; other site 316055001157 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 316055001158 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 316055001159 catalytic residues [active] 316055001160 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 316055001161 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 316055001162 putative active site [active] 316055001163 oxyanion strand; other site 316055001164 catalytic triad [active] 316055001165 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 316055001166 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 316055001167 putative active site pocket [active] 316055001168 4-fold oligomerization interface [polypeptide binding]; other site 316055001169 metal binding residues [ion binding]; metal-binding site 316055001170 3-fold/trimer interface [polypeptide binding]; other site 316055001171 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 316055001172 active site 316055001173 HslU subunit interaction site [polypeptide binding]; other site 316055001174 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 316055001175 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 316055001176 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055001177 Walker A motif; other site 316055001178 ATP binding site [chemical binding]; other site 316055001179 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 316055001180 Walker B motif; other site 316055001181 arginine finger; other site 316055001182 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 316055001183 Smr domain; Region: Smr; pfam01713 316055001184 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 316055001185 MltA specific insert domain; Region: MltA; smart00925 316055001186 3D domain; Region: 3D; pfam06725 316055001187 Tim44-like domain; Region: Tim44; pfam04280 316055001188 preprotein translocase subunit SecB; Validated; Region: PRK05751 316055001189 SecA binding site; other site 316055001190 Preprotein binding site; other site 316055001191 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 316055001192 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 316055001193 active site 316055001194 catalytic site [active] 316055001195 substrate binding site [chemical binding]; other site 316055001196 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 316055001197 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 316055001198 CoA-binding site [chemical binding]; other site 316055001199 ATP-binding [chemical binding]; other site 316055001200 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 316055001201 active site 316055001202 dimer interface [polypeptide binding]; other site 316055001203 PEP synthetase regulatory protein; Provisional; Region: PRK05339 316055001204 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 316055001205 transcription termination factor Rho; Provisional; Region: rho; PRK09376 316055001206 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 316055001207 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 316055001208 RNA binding site [nucleotide binding]; other site 316055001209 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 316055001210 multimer interface [polypeptide binding]; other site 316055001211 Walker A motif; other site 316055001212 ATP binding site [chemical binding]; other site 316055001213 Walker B motif; other site 316055001214 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 316055001215 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 316055001216 trmE is a tRNA modification GTPase; Region: trmE; cd04164 316055001217 G1 box; other site 316055001218 GTP/Mg2+ binding site [chemical binding]; other site 316055001219 Switch I region; other site 316055001220 G2 box; other site 316055001221 Switch II region; other site 316055001222 G3 box; other site 316055001223 G4 box; other site 316055001224 G5 box; other site 316055001225 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 316055001226 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 316055001227 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 316055001228 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 316055001229 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 316055001230 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 316055001231 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 316055001232 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055001233 P-loop; other site 316055001234 Magnesium ion binding site [ion binding]; other site 316055001235 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055001236 Magnesium ion binding site [ion binding]; other site 316055001237 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 316055001238 ParB-like nuclease domain; Region: ParB; smart00470 316055001239 KorB domain; Region: KorB; pfam08535 316055001240 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 316055001241 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 316055001242 Lipopolysaccharide-assembly; Region: LptE; pfam04390 316055001243 Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: LeuS; COG0495 316055001244 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 316055001245 HIGH motif; other site 316055001246 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 316055001247 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316055001248 active site 316055001249 KMSKS motif; other site 316055001250 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 316055001251 tRNA binding surface [nucleotide binding]; other site 316055001252 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055001253 dimerization interface [polypeptide binding]; other site 316055001254 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055001255 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055001256 metal binding site [ion binding]; metal-binding site 316055001257 active site 316055001258 I-site; other site 316055001259 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 316055001260 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 316055001261 catalytic residue [active] 316055001262 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 316055001263 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055001264 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 316055001265 active site 316055001266 phosphorylation site [posttranslational modification] 316055001267 intermolecular recognition site; other site 316055001268 dimerization interface [polypeptide binding]; other site 316055001269 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055001270 DNA binding site [nucleotide binding] 316055001271 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055001272 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 316055001273 ligand binding site [chemical binding]; other site 316055001274 flexible hinge region; other site 316055001275 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 316055001276 putative catalytic site [active] 316055001277 putative phosphate binding site [ion binding]; other site 316055001278 active site 316055001279 metal binding site A [ion binding]; metal-binding site 316055001280 DNA binding site [nucleotide binding] 316055001281 putative AP binding site [nucleotide binding]; other site 316055001282 putative metal binding site B [ion binding]; other site 316055001283 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 316055001284 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 316055001285 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 316055001286 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 316055001287 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 316055001288 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 316055001289 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 316055001290 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 316055001291 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055001292 homodimer interface [polypeptide binding]; other site 316055001293 catalytic residue [active] 316055001294 Protein of unknown function DUF86; Region: DUF86; cl01031 316055001295 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 316055001296 active site 316055001297 NTP binding site [chemical binding]; other site 316055001298 metal binding triad [ion binding]; metal-binding site 316055001299 antibiotic binding site [chemical binding]; other site 316055001300 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 316055001301 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 316055001302 Nitrogen regulatory protein P-II; Region: P-II; smart00938 316055001303 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 316055001304 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 316055001305 Nitrogen regulatory protein P-II; Region: P-II; smart00938 316055001306 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 316055001307 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 316055001308 active site 316055001309 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 316055001310 catalytic triad [active] 316055001311 dimer interface [polypeptide binding]; other site 316055001312 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07333 316055001313 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055001314 Uncharacterized conserved protein [Function unknown]; Region: COG2835 316055001315 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 316055001316 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 316055001317 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 316055001318 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 316055001319 dimerization interface [polypeptide binding]; other site 316055001320 B12 binding domain; Region: B12-binding_2; pfam02607 316055001321 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 316055001322 putative chaperone; Provisional; Region: PRK11678 316055001323 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 316055001324 nucleotide binding site [chemical binding]; other site 316055001325 putative NEF/HSP70 interaction site [polypeptide binding]; other site 316055001326 SBD interface [polypeptide binding]; other site 316055001327 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 316055001328 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 316055001329 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 316055001330 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 316055001331 RNA binding site [nucleotide binding]; other site 316055001332 epoxide hydrolase N-terminal domain-like phosphatase; Region: HAD-1A3-hyp; TIGR02247 316055001333 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 316055001334 motif II; other site 316055001335 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055001336 AAA domain; Region: AAA_14; pfam13173 316055001337 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 316055001338 VWA-like domain (DUF2201); Region: DUF2201; pfam09967 316055001339 metal ion-dependent adhesion site (MIDAS); other site 316055001340 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 316055001341 Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism]; Region: RbcL; COG1850 316055001342 dimer interface [polypeptide binding]; other site 316055001343 catalytic residue [active] 316055001344 metal binding site [ion binding]; metal-binding site 316055001345 Uncharacterized conserved protein [Function unknown]; Region: COG0432 316055001346 hypothetical protein; Provisional; Region: PRK01842 316055001347 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 316055001348 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055001349 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055001350 Walker A/P-loop; other site 316055001351 ATP binding site [chemical binding]; other site 316055001352 Q-loop/lid; other site 316055001353 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055001354 ABC transporter signature motif; other site 316055001355 Walker B; other site 316055001356 D-loop; other site 316055001357 ABC transporter; Region: ABC_tran_2; pfam12848 316055001358 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055001359 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 316055001360 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 316055001361 catalytic site [active] 316055001362 putative active site [active] 316055001363 putative substrate binding site [chemical binding]; other site 316055001364 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 316055001365 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 316055001366 OstA-like protein; Region: OstA; pfam03968 316055001367 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 316055001368 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 316055001369 Walker A/P-loop; other site 316055001370 ATP binding site [chemical binding]; other site 316055001371 Q-loop/lid; other site 316055001372 ABC transporter signature motif; other site 316055001373 Walker B; other site 316055001374 D-loop; other site 316055001375 H-loop/switch region; other site 316055001376 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 316055001377 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 316055001378 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 316055001379 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 316055001380 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 316055001381 30S subunit binding site; other site 316055001382 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 316055001383 active site 316055001384 phosphorylation site [posttranslational modification] 316055001385 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 316055001386 Protein of unknown function (DUF1150); Region: DUF1150; pfam06620 316055001387 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 316055001388 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 316055001389 putative dimer interface [polypeptide binding]; other site 316055001390 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 316055001391 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 316055001392 Walker A/P-loop; other site 316055001393 ATP binding site [chemical binding]; other site 316055001394 Q-loop/lid; other site 316055001395 ABC transporter signature motif; other site 316055001396 Walker B; other site 316055001397 D-loop; other site 316055001398 H-loop/switch region; other site 316055001399 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 316055001400 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055001401 dimer interface [polypeptide binding]; other site 316055001402 conserved gate region; other site 316055001403 putative PBP binding loops; other site 316055001404 ABC-ATPase subunit interface; other site 316055001405 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 316055001406 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055001407 putative PBP binding loops; other site 316055001408 ABC-ATPase subunit interface; other site 316055001409 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316055001410 putative active site [active] 316055001411 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 316055001412 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 316055001413 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 316055001414 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055001415 Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Region: GIY-YIG_SLX1_like; cd10449 316055001416 GIY-YIG motif/motif A; other site 316055001417 putative active site [active] 316055001418 putative metal binding site [ion binding]; other site 316055001419 TIGR02300 family protein; Region: FYDLN_acid 316055001420 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 316055001421 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 316055001422 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 316055001423 hinge; other site 316055001424 active site 316055001425 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 316055001426 putative acyl-acceptor binding pocket; other site 316055001427 cytidylate kinase; Provisional; Region: cmk; PRK00023 316055001428 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 316055001429 CMP-binding site; other site 316055001430 The sites determining sugar specificity; other site 316055001431 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 316055001432 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 316055001433 RNA binding site [nucleotide binding]; other site 316055001434 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 316055001435 RNA binding site [nucleotide binding]; other site 316055001436 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 316055001437 RNA binding site [nucleotide binding]; other site 316055001438 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 316055001439 RNA binding site [nucleotide binding]; other site 316055001440 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 316055001441 RNA binding site [nucleotide binding]; other site 316055001442 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 316055001443 RNA binding site [nucleotide binding]; other site 316055001444 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 316055001445 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 316055001446 tandem repeat interface [polypeptide binding]; other site 316055001447 oligomer interface [polypeptide binding]; other site 316055001448 active site residues [active] 316055001449 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 316055001450 IHF dimer interface [polypeptide binding]; other site 316055001451 IHF - DNA interface [nucleotide binding]; other site 316055001452 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 316055001453 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 316055001454 active site 316055001455 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 316055001456 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 316055001457 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055001458 catalytic residue [active] 316055001459 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 316055001460 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 316055001461 substrate binding site [chemical binding]; other site 316055001462 active site 316055001463 catalytic residues [active] 316055001464 heterodimer interface [polypeptide binding]; other site 316055001465 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 316055001466 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 316055001467 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 316055001468 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055001469 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 316055001470 S-adenosylmethionine binding site [chemical binding]; other site 316055001471 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 316055001472 catalytic residues [active] 316055001473 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 316055001474 Part of AAA domain; Region: AAA_19; pfam13245 316055001475 Family description; Region: UvrD_C_2; pfam13538 316055001476 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 316055001477 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 316055001478 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 316055001479 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 316055001480 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 316055001481 Substrate binding site; other site 316055001482 metal-binding site 316055001483 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 316055001484 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 316055001485 Phosphotransferase enzyme family; Region: APH; pfam01636 316055001486 PAS fold; Region: PAS_7; pfam12860 316055001487 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 316055001488 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055001489 dimer interface [polypeptide binding]; other site 316055001490 phosphorylation site [posttranslational modification] 316055001491 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 316055001492 ATP binding site [chemical binding]; other site 316055001493 Mg2+ binding site [ion binding]; other site 316055001494 G-X-G motif; other site 316055001495 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 316055001496 trimer interface [polypeptide binding]; other site 316055001497 active site 316055001498 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional; Region: PRK13982 316055001499 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 316055001500 Flavoprotein; Region: Flavoprotein; pfam02441 316055001501 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 316055001502 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 316055001503 ABC1 family; Region: ABC1; cl17513 316055001504 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 316055001505 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 316055001506 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 316055001507 S-adenosylmethionine binding site [chemical binding]; other site 316055001508 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 316055001509 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 316055001510 DNA binding site [nucleotide binding] 316055001511 catalytic residue [active] 316055001512 H2TH interface [polypeptide binding]; other site 316055001513 putative catalytic residues [active] 316055001514 turnover-facilitating residue; other site 316055001515 intercalation triad [nucleotide binding]; other site 316055001516 8OG recognition residue [nucleotide binding]; other site 316055001517 putative reading head residues; other site 316055001518 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 316055001519 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 316055001520 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 316055001521 malonyl-CoA synthase; Validated; Region: PRK07514 316055001522 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 316055001523 acyl-activating enzyme (AAE) consensus motif; other site 316055001524 active site 316055001525 AMP binding site [chemical binding]; other site 316055001526 CoA binding site [chemical binding]; other site 316055001527 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 316055001528 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055001529 NAD(P) binding site [chemical binding]; other site 316055001530 active site 316055001531 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 316055001532 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 316055001533 non-specific DNA binding site [nucleotide binding]; other site 316055001534 salt bridge; other site 316055001535 sequence-specific DNA binding site [nucleotide binding]; other site 316055001536 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 316055001537 ADP binding site [chemical binding]; other site 316055001538 magnesium binding site [ion binding]; other site 316055001539 putative shikimate binding site; other site 316055001540 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 316055001541 Fasciclin domain; Region: Fasciclin; pfam02469 316055001542 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 316055001543 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 316055001544 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 316055001545 Moco binding site; other site 316055001546 metal coordination site [ion binding]; other site 316055001547 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 316055001548 tartrate dehydrogenase; Region: TTC; TIGR02089 316055001549 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 316055001550 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 316055001551 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 316055001552 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 316055001553 hypothetical protein; Provisional; Region: PRK05208 316055001554 Helix-turn-helix domain; Region: HTH_18; pfam12833 316055001555 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 316055001556 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 316055001557 DNA binding site [nucleotide binding] 316055001558 active site 316055001559 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 316055001560 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 316055001561 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316055001562 minor groove reading motif; other site 316055001563 helix-hairpin-helix signature motif; other site 316055001564 substrate binding pocket [chemical binding]; other site 316055001565 active site 316055001566 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 316055001567 CysZ-like protein; Reviewed; Region: PRK12768 316055001568 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 316055001569 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 316055001570 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 316055001571 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 316055001572 putative tRNA-binding site [nucleotide binding]; other site 316055001573 B3/4 domain; Region: B3_4; pfam03483 316055001574 tRNA synthetase B5 domain; Region: B5; smart00874 316055001575 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 316055001576 dimer interface [polypeptide binding]; other site 316055001577 motif 1; other site 316055001578 motif 3; other site 316055001579 motif 2; other site 316055001580 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 316055001581 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 316055001582 phenylalanyl-tRNA synthetase, alpha subunit; Region: pheS; TIGR00468 316055001583 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 316055001584 dimer interface [polypeptide binding]; other site 316055001585 motif 1; other site 316055001586 active site 316055001587 motif 2; other site 316055001588 motif 3; other site 316055001589 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 316055001590 23S rRNA binding site [nucleotide binding]; other site 316055001591 L21 binding site [polypeptide binding]; other site 316055001592 L13 binding site [polypeptide binding]; other site 316055001593 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 316055001594 translation initiation factor IF-3; Region: infC; TIGR00168 316055001595 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 316055001596 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 316055001597 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055001598 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 316055001599 epoxyqueuosine reductase; Region: TIGR00276 316055001600 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 316055001601 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055001602 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 316055001603 C-terminal domain interface [polypeptide binding]; other site 316055001604 GSH binding site (G-site) [chemical binding]; other site 316055001605 dimer interface [polypeptide binding]; other site 316055001606 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 316055001607 N-terminal domain interface [polypeptide binding]; other site 316055001608 dimer interface [polypeptide binding]; other site 316055001609 substrate binding pocket (H-site) [chemical binding]; other site 316055001610 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 316055001611 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 316055001612 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 316055001613 putative NAD(P) binding site [chemical binding]; other site 316055001614 active site 316055001615 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055001616 active site 316055001617 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055001618 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055001619 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055001620 dimer interface [polypeptide binding]; other site 316055001621 putative CheW interface [polypeptide binding]; other site 316055001622 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 316055001623 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 316055001624 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 316055001625 Iron-sulfur protein interface; other site 316055001626 proximal quinone binding site [chemical binding]; other site 316055001627 SdhD (CybS) interface [polypeptide binding]; other site 316055001628 proximal heme binding site [chemical binding]; other site 316055001629 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 316055001630 putative SdhC subunit interface [polypeptide binding]; other site 316055001631 putative proximal heme binding site [chemical binding]; other site 316055001632 putative Iron-sulfur protein interface [polypeptide binding]; other site 316055001633 putative proximal quinone binding site; other site 316055001634 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 316055001635 L-aspartate oxidase; Provisional; Region: PRK06175 316055001636 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 316055001637 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 316055001638 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 316055001639 catalytic loop [active] 316055001640 iron binding site [ion binding]; other site 316055001641 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 316055001642 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055001643 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055001644 ligand binding site [chemical binding]; other site 316055001645 MAPEG family; Region: MAPEG; pfam01124 316055001646 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 316055001647 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 316055001648 FtsX-like permease family; Region: FtsX; pfam02687 316055001649 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055001650 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055001651 Walker A/P-loop; other site 316055001652 ATP binding site [chemical binding]; other site 316055001653 Q-loop/lid; other site 316055001654 ABC transporter signature motif; other site 316055001655 Walker B; other site 316055001656 D-loop; other site 316055001657 H-loop/switch region; other site 316055001658 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 316055001659 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 316055001660 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 316055001661 N-terminal plug; other site 316055001662 ligand-binding site [chemical binding]; other site 316055001663 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055001664 ABC-ATPase subunit interface; other site 316055001665 dimer interface [polypeptide binding]; other site 316055001666 putative PBP binding regions; other site 316055001667 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 316055001668 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316055001669 Walker A/P-loop; other site 316055001670 ATP binding site [chemical binding]; other site 316055001671 Q-loop/lid; other site 316055001672 ABC transporter signature motif; other site 316055001673 Walker B; other site 316055001674 D-loop; other site 316055001675 H-loop/switch region; other site 316055001676 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 316055001677 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 316055001678 intersubunit interface [polypeptide binding]; other site 316055001679 Protein of unknown function (DUF938); Region: DUF938; pfam06080 316055001680 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 316055001681 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055001682 active site 316055001683 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055001684 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055001685 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055001686 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 316055001687 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 316055001688 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 316055001689 active site 316055001690 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055001691 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 316055001692 substrate binding pocket [chemical binding]; other site 316055001693 membrane-bound complex binding site; other site 316055001694 hinge residues; other site 316055001695 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055001696 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055001697 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 316055001698 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 316055001699 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 316055001700 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 316055001701 RNA polymerase sigma factor; Provisional; Region: PRK12515 316055001702 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055001703 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055001704 DNA binding residues [nucleotide binding] 316055001705 osmolarity response regulator; Provisional; Region: ompR; PRK09468 316055001706 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 316055001707 active site 316055001708 phosphorylation site [posttranslational modification] 316055001709 intermolecular recognition site; other site 316055001710 dimerization interface [polypeptide binding]; other site 316055001711 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055001712 DNA binding site [nucleotide binding] 316055001713 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 316055001714 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 316055001715 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055001716 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055001717 dimer interface [polypeptide binding]; other site 316055001718 phosphorylation site [posttranslational modification] 316055001719 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 316055001720 ATP binding site [chemical binding]; other site 316055001721 Mg2+ binding site [ion binding]; other site 316055001722 G-X-G motif; other site 316055001723 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055001724 dimerization interface [polypeptide binding]; other site 316055001725 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055001726 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 316055001727 ATP binding site [chemical binding]; other site 316055001728 Mg2+ binding site [ion binding]; other site 316055001729 G-X-G motif; other site 316055001730 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 316055001731 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 316055001732 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055001733 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 316055001734 putative ligand binding site [chemical binding]; other site 316055001735 Pirin-related protein [General function prediction only]; Region: COG1741 316055001736 Pirin; Region: Pirin; pfam02678 316055001737 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 316055001738 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 316055001739 ATP binding site [chemical binding]; other site 316055001740 active site 316055001741 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 316055001742 substrate binding site [chemical binding]; other site 316055001743 gamma-glutamyl kinase; Provisional; Region: PRK05429 316055001744 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 316055001745 nucleotide binding site [chemical binding]; other site 316055001746 homotetrameric interface [polypeptide binding]; other site 316055001747 putative phosphate binding site [ion binding]; other site 316055001748 putative allosteric binding site; other site 316055001749 PUA domain; Region: PUA; pfam01472 316055001750 GTPase CgtA; Reviewed; Region: obgE; PRK12299 316055001751 GTP1/OBG; Region: GTP1_OBG; pfam01018 316055001752 Obg GTPase; Region: Obg; cd01898 316055001753 G1 box; other site 316055001754 GTP/Mg2+ binding site [chemical binding]; other site 316055001755 Switch I region; other site 316055001756 G2 box; other site 316055001757 G3 box; other site 316055001758 Switch II region; other site 316055001759 G4 box; other site 316055001760 G5 box; other site 316055001761 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 316055001762 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055001763 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055001764 Coenzyme A binding pocket [chemical binding]; other site 316055001765 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 316055001766 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 316055001767 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 316055001768 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 316055001769 nucleotide binding site [chemical binding]; other site 316055001770 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 316055001771 active site 316055001772 DNA binding site [nucleotide binding] 316055001773 Int/Topo IB signature motif; other site 316055001774 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055001775 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055001776 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 316055001777 ATP binding site [chemical binding]; other site 316055001778 putative Mg++ binding site [ion binding]; other site 316055001779 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 316055001780 nucleotide binding region [chemical binding]; other site 316055001781 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 316055001782 ATP-binding site [chemical binding]; other site 316055001783 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 316055001784 DNA methylase; Region: N6_N4_Mtase; pfam01555 316055001785 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 316055001786 DNA methylase; Region: N6_N4_Mtase; pfam01555 316055001787 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 316055001788 ATP binding site [chemical binding]; other site 316055001789 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 316055001790 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 316055001791 putative Mg++ binding site [ion binding]; other site 316055001792 Trp repressor protein; Region: Trp_repressor; cl17266 316055001793 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 316055001794 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 316055001795 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 316055001796 substrate binding site [chemical binding]; other site 316055001797 hexamer interface [polypeptide binding]; other site 316055001798 metal binding site [ion binding]; metal-binding site 316055001799 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055001800 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055001801 NAD synthetase; Reviewed; Region: nadE; PRK00876 316055001802 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 316055001803 homodimer interface [polypeptide binding]; other site 316055001804 NAD binding pocket [chemical binding]; other site 316055001805 ATP binding pocket [chemical binding]; other site 316055001806 Mg binding site [ion binding]; other site 316055001807 active-site loop [active] 316055001808 acyl-CoA ligase (AMP-forming), exosortase A-associated; Region: ligase_PEP_1; TIGR03098 316055001809 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055001810 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_6; cd05922 316055001811 acyl-activating enzyme (AAE) consensus motif; other site 316055001812 acyl-activating enzyme (AAE) consensus motif; other site 316055001813 putative AMP binding site [chemical binding]; other site 316055001814 putative active site [active] 316055001815 putative CoA binding site [chemical binding]; other site 316055001816 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 316055001817 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 316055001818 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 316055001819 active site 316055001820 dimer interface [polypeptide binding]; other site 316055001821 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 316055001822 Ligand Binding Site [chemical binding]; other site 316055001823 Molecular Tunnel; other site 316055001824 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 316055001825 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 316055001826 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 316055001827 substrate binding site [chemical binding]; other site 316055001828 oxyanion hole (OAH) forming residues; other site 316055001829 trimer interface [polypeptide binding]; other site 316055001830 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 316055001831 substrate binding site [chemical binding]; other site 316055001832 oxyanion hole (OAH) forming residues; other site 316055001833 trimer interface [polypeptide binding]; other site 316055001834 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055001835 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 316055001836 Class III alcohol dehydrogenase; Region: Zn_ADH_class_III; cd08279 316055001837 oxidoreductase, Rxyl_3153 family; Region: Rxyl_3153; TIGR03989 316055001838 NAD binding site [chemical binding]; other site 316055001839 catalytic Zn binding site [ion binding]; other site 316055001840 substrate binding site [chemical binding]; other site 316055001841 structural Zn binding site [ion binding]; other site 316055001842 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055001843 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 316055001844 ligand binding site [chemical binding]; other site 316055001845 flexible hinge region; other site 316055001846 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 316055001847 4-hydroxybenzoyl-CoA reductase, beta subunit; Region: 4hydrxCoA_B; TIGR03195 316055001848 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 316055001849 4-hydroxybenzoyl-CoA reductase, alpha subunit; Region: 4hydrxCoA_A; TIGR03194 316055001850 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055001851 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055001852 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 316055001853 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 316055001854 catalytic loop [active] 316055001855 iron binding site [ion binding]; other site 316055001856 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316055001857 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 316055001858 Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase); Region: BCL_4HBCL; cd05959 316055001859 dimer interface [polypeptide binding]; other site 316055001860 acyl-activating enzyme (AAE) consensus motif; other site 316055001861 putative active site [active] 316055001862 putative AMP binding site [chemical binding]; other site 316055001863 putative CoA binding site [chemical binding]; other site 316055001864 chemical substrate binding site [chemical binding]; other site 316055001865 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055001866 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 316055001867 putative ligand binding site [chemical binding]; other site 316055001868 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055001869 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 316055001870 TM-ABC transporter signature motif; other site 316055001871 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055001872 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 316055001873 TM-ABC transporter signature motif; other site 316055001874 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055001875 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055001876 Walker A/P-loop; other site 316055001877 ATP binding site [chemical binding]; other site 316055001878 Q-loop/lid; other site 316055001879 ABC transporter signature motif; other site 316055001880 Walker B; other site 316055001881 D-loop; other site 316055001882 H-loop/switch region; other site 316055001883 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055001884 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055001885 Walker A/P-loop; other site 316055001886 ATP binding site [chemical binding]; other site 316055001887 Q-loop/lid; other site 316055001888 ABC transporter signature motif; other site 316055001889 Walker B; other site 316055001890 D-loop; other site 316055001891 H-loop/switch region; other site 316055001892 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055001893 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 316055001894 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055001895 Coenzyme A binding pocket [chemical binding]; other site 316055001896 Rrf2 family protein; Region: rrf2_super; TIGR00738 316055001897 Transcriptional regulator; Region: Rrf2; pfam02082 316055001898 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 316055001899 diiron binding motif [ion binding]; other site 316055001900 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 316055001901 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 316055001902 TPP-binding site [chemical binding]; other site 316055001903 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 316055001904 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 316055001905 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 316055001906 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 316055001907 dimer interface [polypeptide binding]; other site 316055001908 PYR/PP interface [polypeptide binding]; other site 316055001909 TPP binding site [chemical binding]; other site 316055001910 substrate binding site [chemical binding]; other site 316055001911 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055001912 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 316055001913 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055001914 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 316055001915 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055001916 acyl-activating enzyme (AAE) consensus motif; other site 316055001917 AMP binding site [chemical binding]; other site 316055001918 active site 316055001919 CoA binding site [chemical binding]; other site 316055001920 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 316055001921 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 316055001922 benzoyl-CoA reductase, bcr type, subunit B; Region: benz_CoA_red_B; TIGR02260 316055001923 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 316055001924 benzoyl-CoA reductase, subunit C; Region: benz_CoA_red_C; TIGR02263 316055001925 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 316055001926 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 316055001927 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 316055001928 putative NAD(P) binding site [chemical binding]; other site 316055001929 structural Zn binding site [ion binding]; other site 316055001930 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 316055001931 MarR family; Region: MarR_2; pfam12802 316055001932 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase; Region: benzo_BadH; TIGR03206 316055001933 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055001934 NAD(P) binding site [chemical binding]; other site 316055001935 active site 316055001936 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 316055001937 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 316055001938 substrate binding site [chemical binding]; other site 316055001939 oxyanion hole (OAH) forming residues; other site 316055001940 trimer interface [polypeptide binding]; other site 316055001941 cyclohexanecarboxyl-CoA dehydrogenase; Region: cyc_hxne_CoA_dh; TIGR03207 316055001942 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055001943 active site 316055001944 cyclohexanecarboxylate-CoA ligase; Reviewed; Region: PRK13295 316055001945 Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase); Region: CHC_CoA_lg; cd05903 316055001946 acyl-activating enzyme (AAE) consensus motif; other site 316055001947 putative AMP binding site [chemical binding]; other site 316055001948 putative active site [active] 316055001949 putative CoA binding site [chemical binding]; other site 316055001950 enoyl-CoA hydratase; Provisional; Region: PRK05862 316055001951 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 316055001952 substrate binding site [chemical binding]; other site 316055001953 oxyanion hole (OAH) forming residues; other site 316055001954 trimer interface [polypeptide binding]; other site 316055001955 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 316055001956 active site 316055001957 Zn binding site [ion binding]; other site 316055001958 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055001959 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 316055001960 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 316055001961 metal ion-dependent adhesion site (MIDAS); other site 316055001962 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055001963 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055001964 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055001965 MoxR-like ATPases [General function prediction only]; Region: COG0714 316055001966 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055001967 Walker A motif; other site 316055001968 ATP binding site [chemical binding]; other site 316055001969 Walker B motif; other site 316055001970 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 316055001971 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 316055001972 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 316055001973 K-pathway; other site 316055001974 Binuclear center (active site) [active] 316055001975 Putative proton exit pathway; other site 316055001976 Cytochrome c; Region: Cytochrom_C; pfam00034 316055001977 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 316055001978 Subunit I/III interface [polypeptide binding]; other site 316055001979 Predicted integral membrane protein [Function unknown]; Region: COG5615 316055001980 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001981 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001982 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001983 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055001984 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055001985 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 316055001986 active site 316055001987 phosphorylation site [posttranslational modification] 316055001988 intermolecular recognition site; other site 316055001989 dimerization interface [polypeptide binding]; other site 316055001990 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055001991 DNA binding residues [nucleotide binding] 316055001992 dimerization interface [polypeptide binding]; other site 316055001993 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 316055001994 GAF domain; Region: GAF; pfam01590 316055001995 Phytochrome region; Region: PHY; pfam00360 316055001996 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055001997 dimer interface [polypeptide binding]; other site 316055001998 phosphorylation site [posttranslational modification] 316055001999 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 316055002000 ATP binding site [chemical binding]; other site 316055002001 Mg2+ binding site [ion binding]; other site 316055002002 G-X-G motif; other site 316055002003 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 316055002004 GAF domain; Region: GAF; pfam01590 316055002005 Phytochrome region; Region: PHY; pfam00360 316055002006 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055002007 dimer interface [polypeptide binding]; other site 316055002008 phosphorylation site [posttranslational modification] 316055002009 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 316055002010 ATP binding site [chemical binding]; other site 316055002011 Mg2+ binding site [ion binding]; other site 316055002012 G-X-G motif; other site 316055002013 Response regulator receiver domain; Region: Response_reg; pfam00072 316055002014 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 316055002015 active site 316055002016 phosphorylation site [posttranslational modification] 316055002017 intermolecular recognition site; other site 316055002018 dimerization interface [polypeptide binding]; other site 316055002019 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055002020 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 316055002021 active site 316055002022 phosphorylation site [posttranslational modification] 316055002023 intermolecular recognition site; other site 316055002024 dimerization interface [polypeptide binding]; other site 316055002025 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 316055002026 pyruvate carboxylase; Reviewed; Region: PRK12999 316055002027 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055002028 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055002029 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 316055002030 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 316055002031 active site 316055002032 catalytic residues [active] 316055002033 metal binding site [ion binding]; metal-binding site 316055002034 homodimer binding site [polypeptide binding]; other site 316055002035 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 316055002036 carboxyltransferase (CT) interaction site; other site 316055002037 biotinylation site [posttranslational modification]; other site 316055002038 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 316055002039 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 316055002040 active site 316055002041 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 316055002042 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 316055002043 S-adenosylmethionine binding site [chemical binding]; other site 316055002044 hypothetical protein; Provisional; Region: PRK01254 316055002045 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 316055002046 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 316055002047 Protein required for attachment to host cells; Region: Host_attach; cl02398 316055002048 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055002049 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 316055002050 ATP binding site [chemical binding]; other site 316055002051 Mg2+ binding site [ion binding]; other site 316055002052 G-X-G motif; other site 316055002053 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 316055002054 Ribonuclease P; Region: Ribonuclease_P; cl00457 316055002055 membrane protein insertase; Provisional; Region: PRK01318 316055002056 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 316055002057 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 316055002058 G1 box; other site 316055002059 GTP/Mg2+ binding site [chemical binding]; other site 316055002060 Switch I region; other site 316055002061 G2 box; other site 316055002062 G3 box; other site 316055002063 Switch II region; other site 316055002064 G4 box; other site 316055002065 G5 box; other site 316055002066 Protein of unknown function (DUF423); Region: DUF423; pfam04241 316055002067 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 316055002068 feedback inhibition sensing region; other site 316055002069 homohexameric interface [polypeptide binding]; other site 316055002070 nucleotide binding site [chemical binding]; other site 316055002071 N-acetyl-L-glutamate binding site [chemical binding]; other site 316055002072 Protein of unknown function (DUF1036); Region: DUF1036; cl02296 316055002073 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055002074 Protein of unknown function (DUF1036); Region: DUF1036; pfam06282 316055002075 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 316055002076 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 316055002077 motif II; other site 316055002078 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055002079 GIY-YIG motif/motif A; other site 316055002080 putative active site [active] 316055002081 putative metal binding site [ion binding]; other site 316055002082 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 316055002083 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 316055002084 trimer interface [polypeptide binding]; other site 316055002085 active site 316055002086 substrate binding site [chemical binding]; other site 316055002087 CoA binding site [chemical binding]; other site 316055002088 Protein of unknown function (DUF805); Region: DUF805; pfam05656 316055002089 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 316055002090 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 316055002091 metal binding site [ion binding]; metal-binding site 316055002092 dimer interface [polypeptide binding]; other site 316055002093 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 316055002094 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 316055002095 dimerization interface 3.5A [polypeptide binding]; other site 316055002096 active site 316055002097 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 316055002098 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 316055002099 putative active site [active] 316055002100 substrate binding site [chemical binding]; other site 316055002101 putative cosubstrate binding site; other site 316055002102 catalytic site [active] 316055002103 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 316055002104 substrate binding site [chemical binding]; other site 316055002105 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 316055002106 active site 316055002107 catalytic residues [active] 316055002108 metal binding site [ion binding]; metal-binding site 316055002109 RmuC family; Region: RmuC; pfam02646 316055002110 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 316055002111 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 316055002112 S-adenosylmethionine binding site [chemical binding]; other site 316055002113 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 316055002114 hypothetical protein; Validated; Region: PRK09039 316055002115 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055002116 ligand binding site [chemical binding]; other site 316055002117 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 316055002118 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055002119 Coenzyme A binding pocket [chemical binding]; other site 316055002120 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 316055002121 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055002122 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055002123 Walker A/P-loop; other site 316055002124 ATP binding site [chemical binding]; other site 316055002125 Q-loop/lid; other site 316055002126 ABC transporter signature motif; other site 316055002127 Walker B; other site 316055002128 D-loop; other site 316055002129 H-loop/switch region; other site 316055002130 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 316055002131 Protein of unknown function (DUF1465); Region: DUF1465; pfam07323 316055002132 Protein of unknown function (DUF1192); Region: DUF1192; pfam06698 316055002133 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 316055002134 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 316055002135 NAD(P) binding site [chemical binding]; other site 316055002136 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 316055002137 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 316055002138 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 316055002139 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 316055002140 PAS fold; Region: PAS_3; pfam08447 316055002141 putative active site [active] 316055002142 heme pocket [chemical binding]; other site 316055002143 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055002144 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055002145 metal binding site [ion binding]; metal-binding site 316055002146 active site 316055002147 I-site; other site 316055002148 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 316055002149 Predicted transcriptional regulators [Transcription]; Region: COG1695 316055002150 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 316055002151 Virulence activator alpha C-term; Region: Vir_act_alpha_C; pfam10400 316055002152 SnoaL-like domain; Region: SnoaL_2; pfam12680 316055002153 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 316055002154 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 316055002155 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055002156 active site 316055002157 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 316055002158 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 316055002159 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 316055002160 dimer interface [polypeptide binding]; other site 316055002161 active site 316055002162 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 316055002163 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 316055002164 substrate binding site [chemical binding]; other site 316055002165 oxyanion hole (OAH) forming residues; other site 316055002166 trimer interface [polypeptide binding]; other site 316055002167 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 316055002168 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316055002169 glutathionine S-transferase; Provisional; Region: PRK10542 316055002170 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 316055002171 C-terminal domain interface [polypeptide binding]; other site 316055002172 GSH binding site (G-site) [chemical binding]; other site 316055002173 dimer interface [polypeptide binding]; other site 316055002174 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 316055002175 dimer interface [polypeptide binding]; other site 316055002176 N-terminal domain interface [polypeptide binding]; other site 316055002177 substrate binding pocket (H-site) [chemical binding]; other site 316055002178 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055002179 MarR family; Region: MarR_2; pfam12802 316055002180 glutamate--cysteine ligase; Region: PLN02611 316055002181 PAN domain; Region: PAN_4; pfam14295 316055002182 PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech...; Region: PAN_APPLE; cl00112 316055002183 PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech...; Region: PAN_APPLE; cl00112 316055002184 Winged helix-turn helix; Region: HTH_29; pfam13551 316055002185 Homeodomain-like domain; Region: HTH_23; cl17451 316055002186 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 316055002187 Integrase core domain; Region: rve; pfam00665 316055002188 Integrase core domain; Region: rve_3; pfam13683 316055002189 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 316055002190 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055002191 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 316055002192 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 316055002193 active site 316055002194 dimer interface [polypeptide binding]; other site 316055002195 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 316055002196 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 316055002197 active site 316055002198 FMN binding site [chemical binding]; other site 316055002199 substrate binding site [chemical binding]; other site 316055002200 3Fe-4S cluster binding site [ion binding]; other site 316055002201 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 316055002202 domain interface; other site 316055002203 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 316055002204 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 316055002205 putative dimer interface [polypeptide binding]; other site 316055002206 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 316055002207 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055002208 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 316055002209 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 316055002210 active site 316055002211 tetramer interface; other site 316055002212 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055002213 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055002214 metal binding site [ion binding]; metal-binding site 316055002215 active site 316055002216 I-site; other site 316055002217 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 316055002218 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055002219 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 316055002220 KpsF/GutQ family protein; Region: kpsF; TIGR00393 316055002221 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 316055002222 putative active site [active] 316055002223 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 316055002224 muropeptide transporter; Validated; Region: ampG; cl17669 316055002225 muropeptide transporter; Reviewed; Region: ampG; PRK11902 316055002226 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 316055002227 active site 316055002228 oxyanion hole [active] 316055002229 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 316055002230 catalytic triad [active] 316055002231 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 316055002232 Fic/DOC family; Region: Fic; cl00960 316055002233 Transglycosylase SLT domain; Region: SLT_2; pfam13406 316055002234 murein hydrolase B; Provisional; Region: PRK10760; cl17906 316055002235 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055002236 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 316055002237 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 316055002238 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_22; cd08359 316055002239 putative dimer interface [polypeptide binding]; other site 316055002240 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055002241 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055002242 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055002243 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 316055002244 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 316055002245 active site 316055002246 N-formylglutamate amidohydrolase [Amino acid transport and metabolism]; Region: HutG; COG3741 316055002247 Response regulator receiver domain; Region: Response_reg; pfam00072 316055002248 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 316055002249 active site 316055002250 phosphorylation site [posttranslational modification] 316055002251 intermolecular recognition site; other site 316055002252 dimerization interface [polypeptide binding]; other site 316055002253 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 316055002254 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 316055002255 Pirin-related protein [General function prediction only]; Region: COG1741 316055002256 Pirin; Region: Pirin; pfam02678 316055002257 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055002258 transcriptional regulator; Provisional; Region: PRK10632 316055002259 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 316055002260 putative effector binding pocket; other site 316055002261 dimerization interface [polypeptide binding]; other site 316055002262 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 316055002263 hypothetical protein; Validated; Region: PRK00228 316055002264 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316055002265 Sel1-like repeats; Region: SEL1; smart00671 316055002266 Sel1-like repeats; Region: SEL1; smart00671 316055002267 Sel1-like repeats; Region: SEL1; smart00671 316055002268 Sel1-like repeats; Region: SEL1; smart00671 316055002269 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 316055002270 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; pfam09608 316055002271 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 316055002272 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 316055002273 active site 316055002274 zinc binding site [ion binding]; other site 316055002275 Predicted transcriptional regulator [Transcription]; Region: COG2932 316055002276 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 316055002277 Catalytic site [active] 316055002278 Protein of unknown function (DUF952); Region: DUF952; pfam06108 316055002279 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 316055002280 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 316055002281 quinone interaction residues [chemical binding]; other site 316055002282 active site 316055002283 catalytic residues [active] 316055002284 FMN binding site [chemical binding]; other site 316055002285 substrate binding site [chemical binding]; other site 316055002286 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 316055002287 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 316055002288 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 316055002289 ATP-dependent DNA ligase; Validated; Region: PRK09247 316055002290 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 316055002291 active site 316055002292 DNA binding site [nucleotide binding] 316055002293 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 316055002294 DNA binding site [nucleotide binding] 316055002295 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 316055002296 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055002297 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 316055002298 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 316055002299 TPR motif; other site 316055002300 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 316055002301 S-adenosylmethionine binding site [chemical binding]; other site 316055002302 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055002303 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055002304 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055002305 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055002306 putative ligand binding site [chemical binding]; other site 316055002307 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 316055002308 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 316055002309 putative Mg++ binding site [ion binding]; other site 316055002310 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 316055002311 nucleotide binding region [chemical binding]; other site 316055002312 ATP-binding site [chemical binding]; other site 316055002313 DEAD/H associated; Region: DEAD_assoc; pfam08494 316055002314 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 316055002315 putative active site [active] 316055002316 putative metal binding site [ion binding]; other site 316055002317 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055002318 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055002319 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 316055002320 dimerization interface [polypeptide binding]; other site 316055002321 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 316055002322 EamA-like transporter family; Region: EamA; pfam00892 316055002323 EamA-like transporter family; Region: EamA; pfam00892 316055002324 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 316055002325 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 316055002326 Superinfection immunity protein; Region: Imm_superinfect; pfam14373 316055002327 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 316055002328 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316055002329 active site 316055002330 nucleotide binding site [chemical binding]; other site 316055002331 HIGH motif; other site 316055002332 KMSKS motif; other site 316055002333 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055002334 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 316055002335 substrate binding pocket [chemical binding]; other site 316055002336 membrane-bound complex binding site; other site 316055002337 hinge residues; other site 316055002338 CESA_like_2 is a member of the cellulose synthase superfamily; Region: CESA_like_2; cd06427 316055002339 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 316055002340 DXD motif; other site 316055002341 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 316055002342 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 316055002343 Cu(I) binding site [ion binding]; other site 316055002344 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 316055002345 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 316055002346 dimer interface [polypeptide binding]; other site 316055002347 active site 316055002348 CoA binding pocket [chemical binding]; other site 316055002349 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055002350 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055002351 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 316055002352 putative dimerization interface [polypeptide binding]; other site 316055002353 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 316055002354 Amidohydrolase; Region: Amidohydro_2; pfam04909 316055002355 hypothetical protein; Provisional; Region: PRK09262 316055002356 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 316055002357 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 316055002358 NAD binding site [chemical binding]; other site 316055002359 Domain of unknown function (DUF1932); Region: DUF1932; pfam09130 316055002360 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 316055002361 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 316055002362 active site 316055002363 The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit; Region: PCA_45_Doxase_A; cd07924 316055002364 tetramer interface [polypeptide binding]; other site 316055002365 dimer interface [polypeptide binding]; other site 316055002366 active site 316055002367 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 316055002368 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 316055002369 active site 316055002370 Fe(II) binding site [ion binding]; other site 316055002371 dimer interface [polypeptide binding]; other site 316055002372 tetramer interface [polypeptide binding]; other site 316055002373 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316055002374 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 316055002375 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 316055002376 metal binding site [ion binding]; metal-binding site 316055002377 Predicted membrane protein [Function unknown]; Region: COG1238 316055002378 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 316055002379 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 316055002380 FMN binding site [chemical binding]; other site 316055002381 substrate binding site [chemical binding]; other site 316055002382 putative catalytic residue [active] 316055002383 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 316055002384 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 316055002385 active site 2 [active] 316055002386 Peptidase S8 family domain in Thiazoline oxidase/subtilisin-like proteases; Region: Peptidases_S8_thiazoline_oxidase_subtilisin-like_p; cd07476 316055002387 putative active site [active] 316055002388 putative catalytic triad [active] 316055002389 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055002390 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 316055002391 Walker A/P-loop; other site 316055002392 ATP binding site [chemical binding]; other site 316055002393 Q-loop/lid; other site 316055002394 ABC transporter signature motif; other site 316055002395 Walker B; other site 316055002396 D-loop; other site 316055002397 H-loop/switch region; other site 316055002398 TOBE domain; Region: TOBE; pfam03459 316055002399 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055002400 putative PBP binding loops; other site 316055002401 dimer interface [polypeptide binding]; other site 316055002402 ABC-ATPase subunit interface; other site 316055002403 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 316055002404 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 316055002405 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 316055002406 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 316055002407 molybdenum-pterin binding domain; Region: Mop; TIGR00638 316055002408 TOBE domain; Region: TOBE; cl01440 316055002409 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit [Energy production and conversion]; Region: PorA; COG0674 316055002410 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 316055002411 dimer interface [polypeptide binding]; other site 316055002412 PYR/PP interface [polypeptide binding]; other site 316055002413 TPP binding site [chemical binding]; other site 316055002414 substrate binding site [chemical binding]; other site 316055002415 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 316055002416 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 316055002417 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 316055002418 4Fe-4S binding domain; Region: Fer4_6; pfam12837 316055002419 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 316055002420 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 316055002421 Thiamine pyrophosphate (TPP family), Pyruvate ferredoxin/flavodoxin oxidoreductase (PFOR) subfamily, TPP-binding module; PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea; Region: TPP_PFOR; cd02018 316055002422 dimer interface [polypeptide binding]; other site 316055002423 TPP-binding site [chemical binding]; other site 316055002424 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Provisional; Region: PRK12779 316055002425 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055002426 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055002427 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 316055002428 FAD binding pocket [chemical binding]; other site 316055002429 FAD binding motif [chemical binding]; other site 316055002430 phosphate binding motif [ion binding]; other site 316055002431 beta-alpha-beta structure motif; other site 316055002432 NAD binding pocket [chemical binding]; other site 316055002433 Iron coordination center [ion binding]; other site 316055002434 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 316055002435 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 316055002436 putative substrate binding site [chemical binding]; other site 316055002437 putative ATP binding site [chemical binding]; other site 316055002438 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 316055002439 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 316055002440 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055002441 catalytic residue [active] 316055002442 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 316055002443 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 316055002444 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 316055002445 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 316055002446 substrate binding pocket [chemical binding]; other site 316055002447 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08913 316055002448 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 316055002449 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055002450 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 316055002451 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316055002452 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 316055002453 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055002454 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 316055002455 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 316055002456 Flagellar protein FliS; Region: FliS; cl00654 316055002457 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 316055002458 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 316055002459 flagellin; Provisional; Region: PRK12802 316055002460 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055002461 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 316055002462 RNA polymerase sigma factor; Provisional; Region: PRK12538 316055002463 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055002464 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055002465 DNA binding residues [nucleotide binding] 316055002466 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 316055002467 LrgA family; Region: LrgA; pfam03788 316055002468 LrgB-like family; Region: LrgB; pfam04172 316055002469 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 316055002470 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 316055002471 catalytic residues [active] 316055002472 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316055002473 Domain of unknown function DUF20; Region: UPF0118; pfam01594 316055002474 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 316055002475 Putative zinc-finger; Region: zf-HC2; pfam13490 316055002476 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 316055002477 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 316055002478 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055002479 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055002480 DNA binding residues [nucleotide binding] 316055002481 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 316055002482 GTP cyclohydrolase I; Provisional; Region: PLN03044 316055002483 active site 316055002484 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 316055002485 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 316055002486 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 316055002487 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 316055002488 active site 316055002489 glycogen synthase; Provisional; Region: PRK14099 316055002490 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 316055002491 ADP-binding pocket [chemical binding]; other site 316055002492 homodimer interface [polypeptide binding]; other site 316055002493 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 316055002494 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 316055002495 ligand binding site; other site 316055002496 oligomer interface; other site 316055002497 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 316055002498 dimer interface [polypeptide binding]; other site 316055002499 N-terminal domain interface [polypeptide binding]; other site 316055002500 sulfate 1 binding site; other site 316055002501 FOG: CBS domain [General function prediction only]; Region: COG0517 316055002502 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 316055002503 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 316055002504 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 316055002505 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 316055002506 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 316055002507 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055002508 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 316055002509 putative ADP-binding pocket [chemical binding]; other site 316055002510 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 316055002511 AAA domain; Region: AAA_31; pfam13614 316055002512 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 316055002513 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055002514 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 316055002515 Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; Region: CE4_Mlr8448_like_5s; cd10968 316055002516 putative active site [active] 316055002517 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055002518 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 316055002519 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055002520 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 316055002521 S-adenosylmethionine binding site [chemical binding]; other site 316055002522 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 316055002523 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 316055002524 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 316055002525 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055002526 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 316055002527 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 316055002528 RNA binding surface [nucleotide binding]; other site 316055002529 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 316055002530 active site 316055002531 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 316055002532 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 316055002533 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055002534 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055002535 DNA binding residues [nucleotide binding] 316055002536 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 316055002537 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 316055002538 active site 316055002539 substrate-binding site [chemical binding]; other site 316055002540 metal-binding site [ion binding] 316055002541 ATP binding site [chemical binding]; other site 316055002542 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 316055002543 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 316055002544 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055002545 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 316055002546 active site 316055002547 phosphorylation site [posttranslational modification] 316055002548 intermolecular recognition site; other site 316055002549 dimerization interface [polypeptide binding]; other site 316055002550 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055002551 DNA binding site [nucleotide binding] 316055002552 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 316055002553 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 316055002554 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055002555 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055002556 dimer interface [polypeptide binding]; other site 316055002557 phosphorylation site [posttranslational modification] 316055002558 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 316055002559 ATP binding site [chemical binding]; other site 316055002560 Mg2+ binding site [ion binding]; other site 316055002561 G-X-G motif; other site 316055002562 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 316055002563 Hpr binding site; other site 316055002564 active site 316055002565 homohexamer subunit interaction site [polypeptide binding]; other site 316055002566 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 316055002567 active pocket/dimerization site; other site 316055002568 active site 316055002569 phosphorylation site [posttranslational modification] 316055002570 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 316055002571 dimerization domain swap beta strand [polypeptide binding]; other site 316055002572 regulatory protein interface [polypeptide binding]; other site 316055002573 active site 316055002574 regulatory phosphorylation site [posttranslational modification]; other site 316055002575 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 316055002576 GTP-binding protein LepA; Provisional; Region: PRK05433 316055002577 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 316055002578 G1 box; other site 316055002579 putative GEF interaction site [polypeptide binding]; other site 316055002580 GTP/Mg2+ binding site [chemical binding]; other site 316055002581 Switch I region; other site 316055002582 G2 box; other site 316055002583 G3 box; other site 316055002584 Switch II region; other site 316055002585 G4 box; other site 316055002586 G5 box; other site 316055002587 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 316055002588 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 316055002589 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 316055002590 Protein of unknown function (DUF3018); Region: DUF3018; pfam11455 316055002591 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055002592 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 316055002593 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 316055002594 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 316055002595 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 316055002596 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 316055002597 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055002598 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 316055002599 DEAD-like helicases superfamily; Region: DEXDc; smart00487 316055002600 ATP binding site [chemical binding]; other site 316055002601 Mg++ binding site [ion binding]; other site 316055002602 motif III; other site 316055002603 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 316055002604 nucleotide binding region [chemical binding]; other site 316055002605 ATP-binding site [chemical binding]; other site 316055002606 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 316055002607 RNA binding site [nucleotide binding]; other site 316055002608 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 316055002609 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 316055002610 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 316055002611 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 316055002612 catalytic triad [active] 316055002613 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 316055002614 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 316055002615 FeS/SAM binding site; other site 316055002616 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 316055002617 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; pfam05402 316055002618 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 316055002619 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 316055002620 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 316055002621 acyl-CoA synthetase; Validated; Region: PRK08316 316055002622 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055002623 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055002624 acyl-activating enzyme (AAE) consensus motif; other site 316055002625 acyl-activating enzyme (AAE) consensus motif; other site 316055002626 putative AMP binding site [chemical binding]; other site 316055002627 putative active site [active] 316055002628 putative CoA binding site [chemical binding]; other site 316055002629 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055002630 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 316055002631 putative ligand binding site [chemical binding]; other site 316055002632 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 316055002633 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 316055002634 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055002635 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 316055002636 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 316055002637 Trp docking motif [polypeptide binding]; other site 316055002638 dimer interface [polypeptide binding]; other site 316055002639 active site 316055002640 small subunit binding site [polypeptide binding]; other site 316055002641 c-type cytochrome, methanol metabolism-related; Region: 4cys_cytochr; TIGR03874 316055002642 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein; Region: ABC_peri_MoxJ_2; TIGR03871 316055002643 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055002644 substrate binding pocket [chemical binding]; other site 316055002645 membrane-bound complex binding site; other site 316055002646 hinge residues; other site 316055002647 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 316055002648 active site residue [active] 316055002649 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 316055002650 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 316055002651 chaperonin GroEL; Reviewed; Region: groEL; PRK12852 316055002652 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 316055002653 ring oligomerisation interface [polypeptide binding]; other site 316055002654 ATP/Mg binding site [chemical binding]; other site 316055002655 stacking interactions; other site 316055002656 hinge regions; other site 316055002657 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 316055002658 oligomerisation interface [polypeptide binding]; other site 316055002659 mobile loop; other site 316055002660 roof hairpin; other site 316055002661 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 316055002662 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055002663 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055002664 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 316055002665 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 316055002666 putative active site [active] 316055002667 YdjC motif; other site 316055002668 Mg binding site [ion binding]; other site 316055002669 putative homodimer interface [polypeptide binding]; other site 316055002670 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 316055002671 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 316055002672 Ligand binding site; other site 316055002673 Putative Catalytic site; other site 316055002674 DXD motif; other site 316055002675 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 316055002676 ATP phosphoribosyltransferase catalytic subunit; Provisional; Region: hisG; PRK13583 316055002677 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 316055002678 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 316055002679 motif 1; other site 316055002680 dimer interface [polypeptide binding]; other site 316055002681 active site 316055002682 motif 2; other site 316055002683 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 316055002684 active site 316055002685 motif 3; other site 316055002686 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 316055002687 RNA methyltransferase, RsmE family; Region: TIGR00046 316055002688 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12878 316055002689 UbiA prenyltransferase family; Region: UbiA; pfam01040 316055002690 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 316055002691 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 316055002692 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 316055002693 active site 316055002694 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 316055002695 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 316055002696 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 316055002697 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 316055002698 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 316055002699 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 316055002700 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3908 316055002701 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055002702 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055002703 metal binding site [ion binding]; metal-binding site 316055002704 active site 316055002705 I-site; other site 316055002706 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 316055002707 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 316055002708 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055002709 substrate binding pocket [chemical binding]; other site 316055002710 membrane-bound complex binding site; other site 316055002711 hinge residues; other site 316055002712 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 316055002713 1-aminocyclopropane-1-carboxylate deaminase; Provisional; Region: PRK14045 316055002714 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 316055002715 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055002716 catalytic residue [active] 316055002717 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 316055002718 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055002719 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055002720 active site 316055002721 Cytochrome c; Region: Cytochrom_C; cl11414 316055002722 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055002723 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055002724 metal binding site [ion binding]; metal-binding site 316055002725 active site 316055002726 I-site; other site 316055002727 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 316055002728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055002729 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 316055002730 NAD(P) binding site [chemical binding]; other site 316055002731 active site 316055002732 cyclase homology domain; Region: CHD; cd07302 316055002733 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055002734 nucleotidyl binding site; other site 316055002735 metal binding site [ion binding]; metal-binding site 316055002736 dimer interface [polypeptide binding]; other site 316055002737 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 316055002738 Cytochrome P450; Region: p450; cl12078 316055002739 heat shock protein HtpX; Provisional; Region: PRK01345 316055002740 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 316055002741 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055002742 catalytic residue [active] 316055002743 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 316055002744 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 316055002745 Catalytic site; other site 316055002746 Caspase domain; Region: Peptidase_C14; pfam00656 316055002747 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 316055002748 Ligand binding site; other site 316055002749 Glycosyl transferase family 21; Region: Glyco_transf_21; pfam13506 316055002750 DXD motif; other site 316055002751 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 316055002752 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 316055002753 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 316055002754 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 316055002755 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055002756 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 316055002757 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055002758 Protein export membrane protein; Region: SecD_SecF; cl14618 316055002759 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055002760 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055002761 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055002762 ligand binding site [chemical binding]; other site 316055002763 Caspase domain; Region: Peptidase_C14; pfam00656 316055002764 TPR repeat; Region: TPR_11; pfam13414 316055002765 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 316055002766 binding surface 316055002767 TPR motif; other site 316055002768 TPR repeat; Region: TPR_11; pfam13414 316055002769 TPR repeat; Region: TPR_11; pfam13414 316055002770 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 316055002771 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055002772 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055002773 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 316055002774 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 316055002775 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055002776 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 316055002777 fumarylacetoacetase; Region: PLN02856 316055002778 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 316055002779 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 316055002780 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 316055002781 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 316055002782 dimer interface [polypeptide binding]; other site 316055002783 motif 1; other site 316055002784 motif 2; other site 316055002785 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 316055002786 active site 316055002787 motif 3; other site 316055002788 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 316055002789 anticodon binding site; other site 316055002790 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 316055002791 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 316055002792 inhibitor-cofactor binding pocket; inhibition site 316055002793 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055002794 catalytic residue [active] 316055002795 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 316055002796 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 316055002797 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 316055002798 active site 316055002799 motif I; other site 316055002800 motif II; other site 316055002801 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 316055002802 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 316055002803 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 316055002804 active site 316055002805 phosphorylation site [posttranslational modification] 316055002806 intermolecular recognition site; other site 316055002807 dimerization interface [polypeptide binding]; other site 316055002808 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 316055002809 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055002810 DNA-binding site [nucleotide binding]; DNA binding site 316055002811 RNA-binding motif; other site 316055002812 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055002813 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 316055002814 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 316055002815 GIY-YIG motif/motif A; other site 316055002816 active site 316055002817 catalytic site [active] 316055002818 putative DNA binding site [nucleotide binding]; other site 316055002819 metal binding site [ion binding]; metal-binding site 316055002820 UvrB/uvrC motif; Region: UVR; pfam02151 316055002821 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 316055002822 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 316055002823 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 316055002824 MoaE interaction surface [polypeptide binding]; other site 316055002825 MoeB interaction surface [polypeptide binding]; other site 316055002826 thiocarboxylated glycine; other site 316055002827 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 316055002828 MoaE homodimer interface [polypeptide binding]; other site 316055002829 MoaD interaction [polypeptide binding]; other site 316055002830 active site residues [active] 316055002831 HemK family putative methylases; Region: hemK_fam; TIGR00536 316055002832 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 316055002833 S-adenosylmethionine binding site [chemical binding]; other site 316055002834 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 316055002835 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 316055002836 S-adenosylmethionine binding site [chemical binding]; other site 316055002837 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 316055002838 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 316055002839 RNA binding surface [nucleotide binding]; other site 316055002840 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 316055002841 active site 316055002842 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 316055002843 nucleoside/Zn binding site; other site 316055002844 dimer interface [polypeptide binding]; other site 316055002845 catalytic motif [active] 316055002846 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 316055002847 Predicted transcriptional regulators [Transcription]; Region: COG1695 316055002848 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 316055002849 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 316055002850 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055002851 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 316055002852 active site 1 [active] 316055002853 dimer interface [polypeptide binding]; other site 316055002854 hexamer interface [polypeptide binding]; other site 316055002855 active site 2 [active] 316055002856 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; cd03440 316055002857 active site 2 [active] 316055002858 active site 1 [active] 316055002859 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 316055002860 Aerotolerance regulator N-terminal; Region: BatA; cl06567 316055002861 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 316055002862 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 316055002863 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 316055002864 Protein of unknown function DUF58; Region: DUF58; pfam01882 316055002865 MoxR-like ATPases [General function prediction only]; Region: COG0714 316055002866 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055002867 Walker A motif; other site 316055002868 ATP binding site [chemical binding]; other site 316055002869 Walker B motif; other site 316055002870 arginine finger; other site 316055002871 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 316055002872 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 316055002873 putative active site [active] 316055002874 putative CoA binding site [chemical binding]; other site 316055002875 nudix motif; other site 316055002876 metal binding site [ion binding]; metal-binding site 316055002877 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 316055002878 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 316055002879 active site 316055002880 NTP binding site [chemical binding]; other site 316055002881 metal binding triad [ion binding]; metal-binding site 316055002882 Uncharacterized small protein (DUF2158); Region: DUF2158; cl02293 316055002883 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 316055002884 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 316055002885 FeS/SAM binding site; other site 316055002886 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 316055002887 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 316055002888 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 316055002889 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 316055002890 [2Fe-2S] cluster binding site [ion binding]; other site 316055002891 cytochrome b; Provisional; Region: CYTB; MTH00191 316055002892 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 316055002893 Qi binding site; other site 316055002894 intrachain domain interface; other site 316055002895 interchain domain interface [polypeptide binding]; other site 316055002896 heme bH binding site [chemical binding]; other site 316055002897 heme bL binding site [chemical binding]; other site 316055002898 Qo binding site; other site 316055002899 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; cd00290 316055002900 interchain domain interface [polypeptide binding]; other site 316055002901 intrachain domain interface; other site 316055002902 Qi binding site; other site 316055002903 Qo binding site; other site 316055002904 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 316055002905 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 316055002906 hydrogenase 4 subunit B; Validated; Region: PRK06521 316055002907 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055002908 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 316055002909 NADH dehydrogenase; Region: NADHdh; cl00469 316055002910 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl17899 316055002911 hydrogenase 4 subunit F; Validated; Region: PRK06458 316055002912 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055002913 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 316055002914 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 316055002915 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 316055002916 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]; Region: COG3260 316055002917 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 316055002918 active site 316055002919 catalytic triad [active] 316055002920 oxyanion hole [active] 316055002921 Autotransporter beta-domain; Region: Autotransporter; smart00869 316055002922 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316055002923 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 316055002924 TonB system transport protein ExbD, group 1; Region: ExbD_1; TIGR02803 316055002925 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 316055002926 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 316055002927 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 316055002928 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 316055002929 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 316055002930 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 316055002931 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 316055002932 MgtE intracellular N domain; Region: MgtE_N; cl15244 316055002933 FliG C-terminal domain; Region: FliG_C; pfam01706 316055002934 flagellar assembly protein H; Validated; Region: fliH; PRK06032 316055002935 Flagellar assembly protein FliH; Region: FliH; pfam02108 316055002936 flagellar motor switch protein; Reviewed; Region: PRK08916 316055002937 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 316055002938 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055002939 Walker A motif; other site 316055002940 ATP binding site [chemical binding]; other site 316055002941 Walker B motif; other site 316055002942 arginine finger; other site 316055002943 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055002944 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 316055002945 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055002946 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055002947 AAA domain; Region: AAA_30; pfam13604 316055002948 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]; Region: RecD; COG0507 316055002949 Family description; Region: UvrD_C_2; pfam13538 316055002950 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 316055002951 S-adenosylmethionine binding site [chemical binding]; other site 316055002952 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 316055002953 Ferritin-like domain; Region: Ferritin; pfam00210 316055002954 dimerization interface [polypeptide binding]; other site 316055002955 DPS ferroxidase diiron center [ion binding]; other site 316055002956 ion pore; other site 316055002957 Uncharacterized protein containing double-stranded beta helix domain [Function unknown]; Region: COG4297 316055002958 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 316055002959 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 316055002960 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 316055002961 catalytic site [active] 316055002962 subunit interface [polypeptide binding]; other site 316055002963 Yqey-like protein; Region: YqeY; pfam09424 316055002964 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055002965 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 316055002966 acyl-activating enzyme (AAE) consensus motif; other site 316055002967 AMP binding site [chemical binding]; other site 316055002968 active site 316055002969 CoA binding site [chemical binding]; other site 316055002970 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 316055002971 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 316055002972 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 316055002973 TPP-binding site [chemical binding]; other site 316055002974 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated; Region: PRK08659 316055002975 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 316055002976 dimer interface [polypeptide binding]; other site 316055002977 PYR/PP interface [polypeptide binding]; other site 316055002978 TPP binding site [chemical binding]; other site 316055002979 substrate binding site [chemical binding]; other site 316055002980 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 316055002981 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 316055002982 Ferredoxin [Energy production and conversion]; Region: COG1146 316055002983 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 316055002984 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 316055002985 dimer interface [polypeptide binding]; other site 316055002986 PYR/PP interface [polypeptide binding]; other site 316055002987 TPP binding site [chemical binding]; other site 316055002988 substrate binding site [chemical binding]; other site 316055002989 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 316055002990 TPP-binding site; other site 316055002991 4Fe-4S binding domain; Region: Fer4; pfam00037 316055002992 PaaX-like protein; Region: PaaX; pfam07848 316055002993 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 316055002994 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 316055002995 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 316055002996 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 316055002997 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 316055002998 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 316055002999 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 316055003000 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 316055003001 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 316055003002 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 316055003003 FAD binding pocket [chemical binding]; other site 316055003004 FAD binding motif [chemical binding]; other site 316055003005 phosphate binding motif [ion binding]; other site 316055003006 beta-alpha-beta structure motif; other site 316055003007 NAD(p) ribose binding residues [chemical binding]; other site 316055003008 NAD binding pocket [chemical binding]; other site 316055003009 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 316055003010 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 316055003011 catalytic loop [active] 316055003012 iron binding site [ion binding]; other site 316055003013 EthD domain; Region: EthD; cl17553 316055003014 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase; Provisional; Region: PRK11563 316055003015 N-terminal domain of the monoamine oxidase C dehydratase; Region: ALDH_MaoC-N; cd07128 316055003016 substrate binding site [chemical binding]; other site 316055003017 dimer interface [polypeptide binding]; other site 316055003018 NADP binding site [chemical binding]; other site 316055003019 catalytic residues [active] 316055003020 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 316055003021 active site 2 [active] 316055003022 active site 1 [active] 316055003023 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055003024 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055003025 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055003026 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 316055003027 acyl-activating enzyme (AAE) consensus motif; other site 316055003028 AMP binding site [chemical binding]; other site 316055003029 active site 316055003030 CoA binding site [chemical binding]; other site 316055003031 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 316055003032 CoenzymeA binding site [chemical binding]; other site 316055003033 subunit interaction site [polypeptide binding]; other site 316055003034 PHB binding site; other site 316055003035 enoyl-CoA hydratase; Provisional; Region: PRK08140 316055003036 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 316055003037 substrate binding site [chemical binding]; other site 316055003038 oxyanion hole (OAH) forming residues; other site 316055003039 trimer interface [polypeptide binding]; other site 316055003040 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055003041 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 316055003042 putative ligand binding site [chemical binding]; other site 316055003043 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 316055003044 TM-ABC transporter signature motif; other site 316055003045 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055003046 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 316055003047 TM-ABC transporter signature motif; other site 316055003048 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055003049 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055003050 Walker A/P-loop; other site 316055003051 ATP binding site [chemical binding]; other site 316055003052 Q-loop/lid; other site 316055003053 ABC transporter signature motif; other site 316055003054 Walker B; other site 316055003055 D-loop; other site 316055003056 H-loop/switch region; other site 316055003057 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055003058 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055003059 Walker A/P-loop; other site 316055003060 ATP binding site [chemical binding]; other site 316055003061 Q-loop/lid; other site 316055003062 ABC transporter signature motif; other site 316055003063 Walker B; other site 316055003064 D-loop; other site 316055003065 H-loop/switch region; other site 316055003066 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 316055003067 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 316055003068 motif II; other site 316055003069 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055003070 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 316055003071 active site 316055003072 phosphorylation site [posttranslational modification] 316055003073 intermolecular recognition site; other site 316055003074 dimerization interface [polypeptide binding]; other site 316055003075 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055003076 DNA binding residues [nucleotide binding] 316055003077 dimerization interface [polypeptide binding]; other site 316055003078 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055003079 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 316055003080 ATP binding site [chemical binding]; other site 316055003081 Mg2+ binding site [ion binding]; other site 316055003082 G-X-G motif; other site 316055003083 Animal heme peroxidases and related proteins; Region: An_peroxidase_like; cl14561 316055003084 Animal heme peroxidases and related proteins; Region: An_peroxidase_like; cl14561 316055003085 heme binding site [chemical binding]; other site 316055003086 substrate binding site [chemical binding]; other site 316055003087 Animal heme peroxidases and related proteins; Region: An_peroxidase_like; cl14561 316055003088 Animal heme peroxidases and related proteins; Region: An_peroxidase_like; cl14561 316055003089 heme binding site [chemical binding]; other site 316055003090 substrate binding site [chemical binding]; other site 316055003091 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 316055003092 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 316055003093 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055003094 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 316055003095 Walker A/P-loop; other site 316055003096 ATP binding site [chemical binding]; other site 316055003097 Q-loop/lid; other site 316055003098 ABC transporter signature motif; other site 316055003099 Walker B; other site 316055003100 D-loop; other site 316055003101 H-loop/switch region; other site 316055003102 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 316055003103 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 316055003104 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055003105 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055003106 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 316055003107 Transposase; Region: DDE_Tnp_ISL3; pfam01610 316055003108 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316055003109 Transposase; Region: HTH_Tnp_1; pfam01527 316055003110 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 316055003111 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055003112 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 316055003113 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055003114 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 316055003115 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055003116 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055003117 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055003118 Walker A motif; other site 316055003119 ATP binding site [chemical binding]; other site 316055003120 Walker B motif; other site 316055003121 arginine finger; other site 316055003122 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 316055003123 Protein of unknown function DUF262; Region: DUF262; pfam03235 316055003124 Uncharacterized conserved protein [Function unknown]; Region: COG1479 316055003125 Protein of unknown function DUF262; Region: DUF262; pfam03235 316055003126 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 316055003127 Conjugal transfer protein TraD; Region: TraD; pfam06412 316055003128 Conjugal transfer protein TraD; Region: TraD; pfam06412 316055003129 conjugal transfer relaxase TraA; Provisional; Region: PRK13889 316055003130 MobA/MobL family; Region: MobA_MobL; pfam03389 316055003131 AAA domain; Region: AAA_30; pfam13604 316055003132 Family description; Region: UvrD_C_2; pfam13538 316055003133 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 316055003134 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055003135 AAA domain; Region: AAA_23; pfam13476 316055003136 Walker A/P-loop; other site 316055003137 ATP binding site [chemical binding]; other site 316055003138 NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the...; Region: NTR_like; cl02512 316055003139 Protein of unknown function (DUF3732); Region: DUF3732; pfam12532 316055003140 Transposase domain (DUF772); Region: DUF772; pfam05598 316055003141 CHAT domain; Region: CHAT; cl17868 316055003142 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316055003143 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 316055003144 catalytic residues [active] 316055003145 catalytic nucleophile [active] 316055003146 Recombinase; Region: Recombinase; pfam07508 316055003147 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 316055003148 Transducer of regulated CREB activity, C terminus; Region: TORC_C; pfam12886 316055003149 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 316055003150 S-adenosylmethionine binding site [chemical binding]; other site 316055003151 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 316055003152 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 316055003153 Ligand Binding Site [chemical binding]; other site 316055003154 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 316055003155 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 316055003156 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 316055003157 lytic murein transglycosylase; Region: MltB_2; TIGR02283 316055003158 murein hydrolase B; Provisional; Region: PRK10760; cl17906 316055003159 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055003160 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055003161 Cupin domain; Region: Cupin_2; cl17218 316055003162 Cytochrome c553 [Energy production and conversion]; Region: COG2863 316055003163 Cytochrome c; Region: Cytochrom_C; cl11414 316055003164 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 316055003165 acetolactate synthase, catabolic; Region: acolac_catab; TIGR02418 316055003166 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 316055003167 DDE superfamily endonuclease; Region: DDE_3; pfam13358 316055003168 Winged helix-turn helix; Region: HTH_29; pfam13551 316055003169 Homeodomain-like domain; Region: HTH_23; cl17451 316055003170 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 316055003171 Integrase core domain; Region: rve; pfam00665 316055003172 Integrase core domain; Region: rve_3; pfam13683 316055003173 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 316055003174 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 316055003175 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 316055003176 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 316055003177 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055003178 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 316055003179 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055003180 DNA binding residues [nucleotide binding] 316055003181 DNA primase; Validated; Region: dnaG; PRK05667 316055003182 CHC2 zinc finger; Region: zf-CHC2; cl17510 316055003183 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 316055003184 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 316055003185 active site 316055003186 metal binding site [ion binding]; metal-binding site 316055003187 interdomain interaction site; other site 316055003188 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 316055003189 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 316055003190 putative active site pocket [active] 316055003191 dimerization interface [polypeptide binding]; other site 316055003192 putative catalytic residue [active] 316055003193 N-formylglutamate amidohydrolase; Region: FGase; cl01522 316055003194 ATP-dependent Clp protease adaptor; Reviewed; Region: clpS; PRK13019 316055003195 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 316055003196 metal ion-dependent adhesion site (MIDAS); other site 316055003197 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 316055003198 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055003199 S-adenosylmethionine binding site [chemical binding]; other site 316055003200 multidrug efflux protein; Reviewed; Region: PRK01766 316055003201 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 316055003202 cation binding site [ion binding]; other site 316055003203 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 316055003204 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 316055003205 RNA binding surface [nucleotide binding]; other site 316055003206 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 316055003207 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; pfam05014 316055003208 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 316055003209 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 316055003210 TPP-binding site; other site 316055003211 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 316055003212 PYR/PP interface [polypeptide binding]; other site 316055003213 dimer interface [polypeptide binding]; other site 316055003214 TPP binding site [chemical binding]; other site 316055003215 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055003216 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 316055003217 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 316055003218 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 316055003219 putative active site [active] 316055003220 Zn binding site [ion binding]; other site 316055003221 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 316055003222 Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain; Region: MPP_YhcR_N; cd07412 316055003223 putative active site [active] 316055003224 putative metal binding site [ion binding]; other site 316055003225 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 316055003226 Carboxylesterase family; Region: COesterase; pfam00135 316055003227 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 316055003228 substrate binding pocket [chemical binding]; other site 316055003229 catalytic triad [active] 316055003230 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 316055003231 Uncharacterized conserved protein [Function unknown]; Region: COG5361 316055003232 Protein of unknown function (DUF1214); Region: DUF1214; pfam06742 316055003233 enoyl-CoA hydratase; Provisional; Region: PRK06688 316055003234 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 316055003235 substrate binding site [chemical binding]; other site 316055003236 oxyanion hole (OAH) forming residues; other site 316055003237 trimer interface [polypeptide binding]; other site 316055003238 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055003239 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055003240 active site 316055003241 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 316055003242 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 316055003243 active site 316055003244 DNA binding site [nucleotide binding] 316055003245 Int/Topo IB signature motif; other site 316055003246 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316055003247 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 316055003248 catalytic residues [active] 316055003249 catalytic nucleophile [active] 316055003250 Recombinase; Region: Recombinase; pfam07508 316055003251 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 316055003252 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055003253 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055003254 UDP-glucose 4-epimerase; Region: PLN02240 316055003255 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 316055003256 NAD binding site [chemical binding]; other site 316055003257 homodimer interface [polypeptide binding]; other site 316055003258 active site 316055003259 substrate binding site [chemical binding]; other site 316055003260 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 316055003261 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional; Region: PRK13625 316055003262 active site 316055003263 metal binding site [ion binding]; metal-binding site 316055003264 Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction; Region: CysPc; cl00051 316055003265 catalytic site [active] 316055003266 A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine...; Region: Peptidase_C39_likeA; cd02417 316055003267 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 316055003268 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055003269 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055003270 Walker A/P-loop; other site 316055003271 ATP binding site [chemical binding]; other site 316055003272 Q-loop/lid; other site 316055003273 ABC transporter signature motif; other site 316055003274 Walker B; other site 316055003275 D-loop; other site 316055003276 H-loop/switch region; other site 316055003277 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 316055003278 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055003279 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055003280 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 316055003281 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055003282 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 316055003283 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 316055003284 AAA ATPase domain; Region: AAA_16; pfam13191 316055003285 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316055003286 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 316055003287 SLBB domain; Region: SLBB; pfam10531 316055003288 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 316055003289 Bacterial sugar transferase; Region: Bac_transf; pfam02397 316055003290 TPR repeat; Region: TPR_11; pfam13414 316055003291 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 316055003292 TPR motif; other site 316055003293 binding surface 316055003294 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 316055003295 binding surface 316055003296 TPR motif; other site 316055003297 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 316055003298 TPR motif; other site 316055003299 binding surface 316055003300 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 316055003301 TPR motif; other site 316055003302 binding surface 316055003303 Tetratricopeptide repeat; Region: TPR_16; pfam13432 316055003304 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 316055003305 TPR motif; other site 316055003306 binding surface 316055003307 Tetratricopeptide repeat; Region: TPR_16; pfam13432 316055003308 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 316055003309 exosortase D, VPLPA-CTERM-specific; Region: exosort_VPLPA; TIGR04152 316055003310 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 316055003311 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 316055003312 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 316055003313 anti sigma factor interaction site; other site 316055003314 regulatory phosphorylation site [posttranslational modification]; other site 316055003315 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 316055003316 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 316055003317 DXD motif; other site 316055003318 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 316055003319 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055003320 NAD binding site [chemical binding]; other site 316055003321 putative substrate binding site 2 [chemical binding]; other site 316055003322 putative substrate binding site 1 [chemical binding]; other site 316055003323 active site 316055003324 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055003325 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 316055003326 colanic acid biosynthesis glycosyltransferase WcaL; Provisional; Region: PRK15427 316055003327 This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor; Region: GT1_amsK_like; cd03799 316055003328 putative ADP-binding pocket [chemical binding]; other site 316055003329 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 316055003330 active site 316055003331 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055003332 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 316055003333 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 316055003334 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 316055003335 Lyase; Region: Lyase_1; pfam00206 316055003336 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 316055003337 O-Antigen ligase; Region: Wzy_C; pfam04932 316055003338 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 316055003339 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 316055003340 VPLPA-CTERM protein sorting domain; Region: VPLPA-CTERM; TIGR03370 316055003341 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055003342 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055003343 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 316055003344 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 316055003345 Integrase core domain; Region: rve; pfam00665 316055003346 DNA polymerase III subunit delta'; Validated; Region: PRK09112 316055003347 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 316055003348 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 316055003349 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316055003350 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 316055003351 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055003352 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055003353 DNA binding residues [nucleotide binding] 316055003354 dimerization interface [polypeptide binding]; other site 316055003355 PilZ domain; Region: PilZ; pfam07238 316055003356 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055003357 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 316055003358 Walker A motif; other site 316055003359 ATP binding site [chemical binding]; other site 316055003360 Walker B motif; other site 316055003361 arginine finger; other site 316055003362 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 316055003363 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055003364 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055003365 Transposase; Region: HTH_Tnp_1; cl17663 316055003366 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316055003367 Transposase; Region: HTH_Tnp_1; pfam01527 316055003368 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 316055003369 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055003370 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 316055003371 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055003372 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 316055003373 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055003374 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055003375 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055003376 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055003377 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 316055003378 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 316055003379 Transposase, Mutator family; Region: Transposase_mut; pfam00872 316055003380 Transposase domain (DUF772); Region: DUF772; pfam05598 316055003381 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055003382 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 316055003383 Transposase; Region: HTH_Tnp_1; cl17663 316055003384 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 316055003385 flagellum-specific ATP synthase; Validated; Region: fliI; PRK06002 316055003386 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055003387 Walker A motif; other site 316055003388 ATP binding site [chemical binding]; other site 316055003389 Walker B motif; other site 316055003390 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12642 316055003391 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 316055003392 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055003393 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 316055003394 flagellar motor protein MotA; Validated; Region: PRK09110 316055003395 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 316055003396 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 316055003397 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 316055003398 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 316055003399 FliG C-terminal domain; Region: FliG_C; pfam01706 316055003400 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK13109 316055003401 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 316055003402 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06003 316055003403 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316055003404 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK12782 316055003405 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316055003406 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055003407 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00790 316055003408 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12692 316055003409 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055003410 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK06005 316055003411 flagellar basal body P-ring protein; Reviewed; Region: flgI; PRK12789 316055003412 Flagellar P-ring protein; Region: FlgI; pfam02119 316055003413 Uncharacterized conserved protein [Function unknown]; Region: COG3334 316055003414 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12788 316055003415 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 316055003416 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 316055003417 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK12783 316055003418 flagellin; Reviewed; Region: PRK12687 316055003419 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055003420 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 316055003421 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 316055003422 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 316055003423 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 316055003424 flagellar motor protein MotB; Validated; Region: motB; PRK05996 316055003425 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 316055003426 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055003427 ligand binding site [chemical binding]; other site 316055003428 chemotaxis protein; Reviewed; Region: PRK12798 316055003429 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 316055003430 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 316055003431 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055003432 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055003433 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 316055003434 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316055003435 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 316055003436 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055003437 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 316055003438 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055003439 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 316055003440 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055003441 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 316055003442 flagellar biosynthesis regulatory protein FlaF; Reviewed; Region: flaF; PRK12793 316055003443 Flagellar protein FlaF; Region: FlaF; pfam07309 316055003444 flagellar biosynthesis repressor FlbT; Reviewed; Region: flbT; PRK00794 316055003445 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06009 316055003446 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 316055003447 flagellar biosynthesis protein FliQ; Reviewed; Region: fliQ; PRK12781 316055003448 flagellar biosynthesis protein FlhA; Reviewed; Region: flhA; PRK12792 316055003449 FHIPEP family; Region: FHIPEP; pfam00771 316055003450 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK12780 316055003451 Rod binding protein; Region: Rod-binding; pfam10135 316055003452 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055003453 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 316055003454 active site 316055003455 dimerization interface [polypeptide binding]; other site 316055003456 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055003457 DNA binding site [nucleotide binding] 316055003458 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055003459 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 316055003460 putative ADP-binding pocket [chemical binding]; other site 316055003461 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 316055003462 Protein of unknown function, DUF608; Region: DUF608; pfam04685 316055003463 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055003464 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 316055003465 putative substrate translocation pore; other site 316055003466 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 316055003467 Response regulator receiver domain; Region: Response_reg; pfam00072 316055003468 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 316055003469 active site 316055003470 phosphorylation site [posttranslational modification] 316055003471 intermolecular recognition site; other site 316055003472 dimerization interface [polypeptide binding]; other site 316055003473 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 316055003474 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 316055003475 putative binding surface; other site 316055003476 active site 316055003477 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316055003478 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 316055003479 ATP binding site [chemical binding]; other site 316055003480 Mg2+ binding site [ion binding]; other site 316055003481 G-X-G motif; other site 316055003482 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 316055003483 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 316055003484 putative CheA interaction surface; other site 316055003485 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 316055003486 PAS domain; Region: PAS_9; pfam13426 316055003487 putative active site [active] 316055003488 heme pocket [chemical binding]; other site 316055003489 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 316055003490 PAS domain; Region: PAS_9; pfam13426 316055003491 putative active site [active] 316055003492 heme pocket [chemical binding]; other site 316055003493 PAS domain; Region: PAS_9; pfam13426 316055003494 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 316055003495 putative active site [active] 316055003496 heme pocket [chemical binding]; other site 316055003497 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 316055003498 PAS domain; Region: PAS_9; pfam13426 316055003499 putative active site [active] 316055003500 heme pocket [chemical binding]; other site 316055003501 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055003502 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055003503 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055003504 dimer interface [polypeptide binding]; other site 316055003505 putative CheW interface [polypeptide binding]; other site 316055003506 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 316055003507 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316055003508 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 316055003509 CheD chemotactic sensory transduction; Region: CheD; cl00810 316055003510 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 316055003511 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 316055003512 active site 316055003513 phosphorylation site [posttranslational modification] 316055003514 intermolecular recognition site; other site 316055003515 dimerization interface [polypeptide binding]; other site 316055003516 CheB methylesterase; Region: CheB_methylest; pfam01339 316055003517 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 316055003518 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055003519 dimer interface [polypeptide binding]; other site 316055003520 putative CheW interface [polypeptide binding]; other site 316055003521 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 316055003522 anti sigma factor interaction site; other site 316055003523 regulatory phosphorylation site [posttranslational modification]; other site 316055003524 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 316055003525 Response regulator receiver domain; Region: Response_reg; pfam00072 316055003526 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 316055003527 active site 316055003528 phosphorylation site [posttranslational modification] 316055003529 intermolecular recognition site; other site 316055003530 dimerization interface [polypeptide binding]; other site 316055003531 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 316055003532 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 316055003533 putative binding surface; other site 316055003534 active site 316055003535 Cache domain; Region: Cache_1; pfam02743 316055003536 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 316055003537 PAS fold; Region: PAS_3; pfam08447 316055003538 putative active site [active] 316055003539 heme pocket [chemical binding]; other site 316055003540 PAS fold; Region: PAS_7; pfam12860 316055003541 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055003542 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055003543 dimer interface [polypeptide binding]; other site 316055003544 phosphorylation site [posttranslational modification] 316055003545 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 316055003546 ATP binding site [chemical binding]; other site 316055003547 Mg2+ binding site [ion binding]; other site 316055003548 G-X-G motif; other site 316055003549 Response regulator receiver domain; Region: Response_reg; pfam00072 316055003550 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 316055003551 active site 316055003552 phosphorylation site [posttranslational modification] 316055003553 intermolecular recognition site; other site 316055003554 dimerization interface [polypeptide binding]; other site 316055003555 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 316055003556 active site residue [active] 316055003557 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 316055003558 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 316055003559 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 316055003560 [2Fe-2S] cluster binding site [ion binding]; other site 316055003561 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 316055003562 VWA domain containing CoxE-like protein; Region: VWA_CoxE; pfam05762 316055003563 von Willebrand factor (vWF) type A domain; Region: VWA; smart00327 316055003564 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055003565 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 316055003566 Walker A motif; other site 316055003567 ATP binding site [chemical binding]; other site 316055003568 Walker B motif; other site 316055003569 arginine finger; other site 316055003570 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 316055003571 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 316055003572 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055003573 active site 316055003574 ykkC-yxkD element as predicted by Rfam (RF00442) 316055003575 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055003576 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 316055003577 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055003578 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055003579 dimer interface [polypeptide binding]; other site 316055003580 conserved gate region; other site 316055003581 putative PBP binding loops; other site 316055003582 ABC-ATPase subunit interface; other site 316055003583 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055003584 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055003585 Walker A/P-loop; other site 316055003586 ATP binding site [chemical binding]; other site 316055003587 Q-loop/lid; other site 316055003588 ABC transporter signature motif; other site 316055003589 Walker B; other site 316055003590 D-loop; other site 316055003591 H-loop/switch region; other site 316055003592 urea carboxylase-associated protein 2; Region: urea_degr_2; TIGR03425 316055003593 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 316055003594 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 316055003595 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 316055003596 urea carboxylase; Region: urea_carbox; TIGR02712 316055003597 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055003598 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055003599 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 316055003600 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 316055003601 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 316055003602 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 316055003603 carboxyltransferase (CT) interaction site; other site 316055003604 biotinylation site [posttranslational modification]; other site 316055003605 allophanate hydrolase; Provisional; Region: PRK08186 316055003606 Amidase; Region: Amidase; cl11426 316055003607 Domain of Unknown Function with PDB structure (DUF3861); Region: DUF3861; pfam12977 316055003608 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055003609 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055003610 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 316055003611 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055003612 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055003613 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055003614 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 316055003615 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH2; cd08183 316055003616 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 316055003617 putative active site [active] 316055003618 metal binding site [ion binding]; metal-binding site 316055003619 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 316055003620 hydrogenase 2 large subunit; Provisional; Region: PRK10467 316055003621 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 316055003622 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 316055003623 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 316055003624 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 316055003625 hydrogenase 1 large subunit; Provisional; Region: PRK10170 316055003626 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 316055003627 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 316055003628 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 316055003629 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 316055003630 putative substrate-binding site; other site 316055003631 nickel binding site [ion binding]; other site 316055003632 HupF/HypC family; Region: HupF_HypC; pfam01455 316055003633 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 316055003634 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 316055003635 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 316055003636 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 316055003637 Rubredoxin; Region: Rubredoxin; pfam00301 316055003638 iron binding site [ion binding]; other site 316055003639 Protein of unknown function (DUF3457); Region: DUF3457; pfam11939 316055003640 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 316055003641 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 316055003642 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 316055003643 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055003644 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 316055003645 Acylphosphatase; Region: Acylphosphatase; pfam00708 316055003646 HypF finger; Region: zf-HYPF; pfam07503 316055003647 HypF finger; Region: zf-HYPF; pfam07503 316055003648 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 316055003649 HupF/HypC family; Region: HupF_HypC; pfam01455 316055003650 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 316055003651 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 316055003652 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 316055003653 dimerization interface [polypeptide binding]; other site 316055003654 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 316055003655 ATP binding site [chemical binding]; other site 316055003656 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 316055003657 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 316055003658 active site 316055003659 phosphorylation site [posttranslational modification] 316055003660 intermolecular recognition site; other site 316055003661 dimerization interface [polypeptide binding]; other site 316055003662 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055003663 Walker A motif; other site 316055003664 ATP binding site [chemical binding]; other site 316055003665 Walker B motif; other site 316055003666 arginine finger; other site 316055003667 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055003668 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 316055003669 putative active site [active] 316055003670 heme pocket [chemical binding]; other site 316055003671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055003672 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055003673 dimer interface [polypeptide binding]; other site 316055003674 phosphorylation site [posttranslational modification] 316055003675 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 316055003676 ATP binding site [chemical binding]; other site 316055003677 Mg2+ binding site [ion binding]; other site 316055003678 G-X-G motif; other site 316055003679 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 316055003680 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 316055003681 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 316055003682 active site 316055003683 metal binding site [ion binding]; metal-binding site 316055003684 DNA binding site [nucleotide binding] 316055003685 AAA domain; Region: AAA_27; pfam13514 316055003686 benzoylformate decarboxylase; Reviewed; Region: PRK07092 316055003687 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055003688 PYR/PP interface [polypeptide binding]; other site 316055003689 dimer interface [polypeptide binding]; other site 316055003690 TPP binding site [chemical binding]; other site 316055003691 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316055003692 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 316055003693 TPP-binding site [chemical binding]; other site 316055003694 dimer interface [polypeptide binding]; other site 316055003695 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 316055003696 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 316055003697 putative DNA binding site [nucleotide binding]; other site 316055003698 putative Zn2+ binding site [ion binding]; other site 316055003699 AsnC family; Region: AsnC_trans_reg; pfam01037 316055003700 Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a...; Region: Polysulfide_ST; cd01447 316055003701 active site 316055003702 catalytic residue [active] 316055003703 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 316055003704 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 316055003705 [4Fe-4S] binding site [ion binding]; other site 316055003706 molybdopterin cofactor binding site; other site 316055003707 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 316055003708 molybdopterin cofactor binding site; other site 316055003709 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 316055003710 sulfite reductase; Provisional; Region: PRK06214 316055003711 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; cd06199 316055003712 FAD binding pocket [chemical binding]; other site 316055003713 FAD binding motif [chemical binding]; other site 316055003714 catalytic residues [active] 316055003715 NAD binding pocket [chemical binding]; other site 316055003716 phosphate binding motif [ion binding]; other site 316055003717 beta-alpha-beta structure motif; other site 316055003718 ferredoxin-nitrite reductase; Reviewed; Region: nirA; PRK09567 316055003719 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316055003720 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316055003721 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 316055003722 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055003723 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 316055003724 heme-binding site [chemical binding]; other site 316055003725 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 316055003726 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055003727 Walker A/P-loop; other site 316055003728 ATP binding site [chemical binding]; other site 316055003729 Q-loop/lid; other site 316055003730 ABC transporter signature motif; other site 316055003731 Walker B; other site 316055003732 D-loop; other site 316055003733 H-loop/switch region; other site 316055003734 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055003735 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055003736 putative PBP binding loops; other site 316055003737 dimer interface [polypeptide binding]; other site 316055003738 ABC-ATPase subunit interface; other site 316055003739 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055003740 NMT1-like family; Region: NMT1_2; pfam13379 316055003741 NMT1-like family; Region: NMT1_2; pfam13379 316055003742 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055003743 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 316055003744 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 316055003745 active site 316055003746 phosphorylation site [posttranslational modification] 316055003747 intermolecular recognition site; other site 316055003748 ANTAR domain; Region: ANTAR; pfam03861 316055003749 BA14K-like protein; Region: BA14K; pfam07886 316055003750 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 316055003751 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_13; cd08354 316055003752 putative metal binding site [ion binding]; other site 316055003753 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055003754 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 316055003755 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 316055003756 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 316055003757 catalytic site [active] 316055003758 active site 316055003759 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 316055003760 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 316055003761 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 316055003762 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 316055003763 active site 316055003764 catalytic site [active] 316055003765 Response regulator receiver domain; Region: Response_reg; pfam00072 316055003766 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 316055003767 active site 316055003768 phosphorylation site [posttranslational modification] 316055003769 intermolecular recognition site; other site 316055003770 dimerization interface [polypeptide binding]; other site 316055003771 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 316055003772 Protein of unknown function (DUF2974); Region: DUF2974; pfam11187 316055003773 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055003774 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 316055003775 Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]; Region: OtsA; COG0380 316055003776 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 316055003777 active site 316055003778 homotetramer interface [polypeptide binding]; other site 316055003779 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 316055003780 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 316055003781 transmembrane helices; other site 316055003782 phosphoglucomutase; Validated; Region: PRK07564 316055003783 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 316055003784 active site 316055003785 substrate binding site [chemical binding]; other site 316055003786 metal binding site [ion binding]; metal-binding site 316055003787 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 316055003788 Autoinducer binding domain; Region: Autoind_bind; pfam03472 316055003789 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055003790 DNA binding residues [nucleotide binding] 316055003791 dimerization interface [polypeptide binding]; other site 316055003792 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 316055003793 NnrU protein; Region: NnrU; pfam07298 316055003794 NnrS protein; Region: NnrS; pfam05940 316055003795 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 316055003796 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 316055003797 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055003798 active site 316055003799 phosphorylation site [posttranslational modification] 316055003800 intermolecular recognition site; other site 316055003801 dimerization interface [polypeptide binding]; other site 316055003802 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055003803 DNA binding residues [nucleotide binding] 316055003804 dimerization interface [polypeptide binding]; other site 316055003805 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055003806 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055003807 PUCC protein; Region: PUCC; pfam03209 316055003808 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 316055003809 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055003810 Domain of unknown function (DUF2383); Region: DUF2383; pfam09537 316055003811 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; Region: FrhB_FdhB_N; pfam04422 316055003812 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 316055003813 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2343 316055003814 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 316055003815 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055003816 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 316055003817 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 316055003818 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 316055003819 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 316055003820 domain interfaces; other site 316055003821 active site 316055003822 magnesium chelatase subunit I; Provisional; Region: bchI; PRK13407 316055003823 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055003824 Walker A motif; other site 316055003825 ATP binding site [chemical binding]; other site 316055003826 Walker B motif; other site 316055003827 arginine finger; other site 316055003828 magnesium chelatase subunit D; Provisional; Region: bchD; PRK13406 316055003829 Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is...; Region: vWA_Magnesium_chelatase; cd01451 316055003830 metal ion-dependent adhesion site (MIDAS); other site 316055003831 PAS fold; Region: PAS_3; pfam08447 316055003832 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 316055003833 putative active site [active] 316055003834 heme pocket [chemical binding]; other site 316055003835 PAS fold; Region: PAS_3; pfam08447 316055003836 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 316055003837 putative active site [active] 316055003838 heme pocket [chemical binding]; other site 316055003839 Helix-turn-helix domain; Region: HTH_18; pfam12833 316055003840 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055003841 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 316055003842 putative active site [active] 316055003843 heme pocket [chemical binding]; other site 316055003844 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055003845 Helix-turn-helix domain; Region: HTH_18; pfam12833 316055003846 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055003847 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055003848 dimerization interface [polypeptide binding]; other site 316055003849 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055003850 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055003851 dimer interface [polypeptide binding]; other site 316055003852 putative CheW interface [polypeptide binding]; other site 316055003853 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055003854 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055003855 dimerization interface [polypeptide binding]; other site 316055003856 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055003857 dimer interface [polypeptide binding]; other site 316055003858 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055003859 putative CheW interface [polypeptide binding]; other site 316055003860 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 316055003861 substrate binding site [chemical binding]; other site 316055003862 active site 316055003863 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055003864 putative magnesium chelatase accessory protein; Region: bchO_mg_che_rel; TIGR03056 316055003865 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055003866 phytoene desaturase; Region: crtI_fam; TIGR02734 316055003867 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055003868 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 316055003869 active site lid residues [active] 316055003870 substrate binding pocket [chemical binding]; other site 316055003871 catalytic residues [active] 316055003872 substrate-Mg2+ binding site; other site 316055003873 aspartate-rich region 1; other site 316055003874 aspartate-rich region 2; other site 316055003875 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 316055003876 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl17752 316055003877 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 316055003878 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 316055003879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055003880 NADH(P)-binding; Region: NAD_binding_10; pfam13460 316055003881 NAD(P) binding site [chemical binding]; other site 316055003882 active site 316055003883 phytoene desaturase; Region: crtI_fam; TIGR02734 316055003884 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 316055003885 substrate binding pocket [chemical binding]; other site 316055003886 chain length determination region; other site 316055003887 substrate-Mg2+ binding site; other site 316055003888 catalytic residues [active] 316055003889 aspartate-rich region 1; other site 316055003890 active site lid residues [active] 316055003891 aspartate-rich region 2; other site 316055003892 O-methyltransferase; Region: Methyltransf_2; pfam00891 316055003893 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase; Region: bchC; TIGR01202 316055003894 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members; Region: 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_; cd08255 316055003895 putative NAD(P) binding site [chemical binding]; other site 316055003896 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055003897 chlorophyllide reductase iron protein subunit X; Region: BchX; TIGR02016 316055003898 Chlide_reductase_Y : Y subunit of chlorophyllide (chlide) reductase (BchY). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase...; Region: Chlide_reductase_Y; cd01980 316055003899 chlorophyllide reductase subunit Y; Region: BchY; TIGR02015 316055003900 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 316055003901 chlorophyllide reductase subunit Z; Region: BchZ; TIGR02014 316055003902 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055003903 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055003904 Subunit L of bacterial photosynthetic reaction center; Region: Photo-RC_L; cd09290 316055003905 subunit M interface; other site 316055003906 subunit H interface; other site 316055003907 quinone binding site; other site 316055003908 bacteriopheophytin binding site; other site 316055003909 bacteriochlorophyll binding site; other site 316055003910 cytochrome C subunit interface; other site 316055003911 Fe binding site [ion binding]; other site 316055003912 Subunit M of bacterial photosynthetic reaction center; Region: Photo-RC_M; cd09291 316055003913 subunit H interface; other site 316055003914 subunit L interface; other site 316055003915 bacteriopheophytin binding site; other site 316055003916 carotenoid binding site; other site 316055003917 bacteriochlorophyll binding site; other site 316055003918 cytochrome C interface; other site 316055003919 quinone binding site; other site 316055003920 Fe binding site [ion binding]; other site 316055003921 transcriptional regulator PpsR; Region: PpsR-CrtJ; TIGR02040 316055003922 PAS domain; Region: PAS_8; pfam13188 316055003923 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055003924 bacteriochlorophyll/chlorophyll a synthase; Reviewed; Region: PRK07566 316055003925 UbiA prenyltransferase family; Region: UbiA; pfam01040 316055003926 PUCC protein; Region: PUCC; pfam03209 316055003927 geranylgeranyl reductase; Region: BchP-ChlP; TIGR02023 316055003928 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055003929 TspO/MBR family; Region: TspO_MBR; pfam03073 316055003930 Cytochrome c; Region: Cytochrom_C; cl11414 316055003931 transcriptional regulator PpsR; Region: PpsR-CrtJ; TIGR02040 316055003932 PAS domain; Region: PAS_8; pfam13188 316055003933 putative active site [active] 316055003934 heme pocket [chemical binding]; other site 316055003935 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 316055003936 putative active site [active] 316055003937 heme pocket [chemical binding]; other site 316055003938 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055003939 PAS fold; Region: PAS_2; pfam08446 316055003940 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 316055003941 GAF domain; Region: GAF; pfam01590 316055003942 Phytochrome region; Region: PHY; pfam00360 316055003943 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 316055003944 PAS domain; Region: PAS_9; pfam13426 316055003945 putative active site [active] 316055003946 heme pocket [chemical binding]; other site 316055003947 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 316055003948 heme binding pocket [chemical binding]; other site 316055003949 heme ligand [chemical binding]; other site 316055003950 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 316055003951 B12 binding domain; Region: B12-binding_2; pfam02607 316055003952 B12 binding domain; Region: B12-binding; pfam02310 316055003953 B12 binding site [chemical binding]; other site 316055003954 2-vinyl bacteriochlorophyllide hydratase (BCHF); Region: BCHF; pfam07284 316055003955 Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and...; Region: Pchlide_reductase_N; cd01979 316055003956 light-independent protochlorophyllide reductase, N subunit; Region: DPOR_bchN; TIGR01279 316055003957 light-independent protochlorophyllide reductase subunit B; Provisional; Region: PRK02910 316055003958 Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and...; Region: Pchlide_reductase_B; cd01981 316055003959 Proto-chlorophyllide reductase 57 kD subunit; Region: PCP_red; pfam08369 316055003960 magnesium chelatase subunit H; Provisional; Region: bchH; PRK13405 316055003961 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 316055003962 protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional; Region: chlL; PRK13185 316055003963 This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are...; Region: Bchl_like; cd02032 316055003964 Mg-protoporphyrin IX methyl transferase; Validated; Region: PRK07580 316055003965 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055003966 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 316055003967 S-adenosylmethionine binding site [chemical binding]; other site 316055003968 Magnesium-protoporphyrin IX methyltransferase C-terminus; Region: Mg-por_mtran_C; pfam07109 316055003969 PUCC protein; Region: PUCC; pfam03209 316055003970 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 produce...; Region: PRCH; cl17581 316055003971 photosynthetic reaction center, subunit H, bacterial; Region: puhA; TIGR01150 316055003972 subunit M interaction residues [polypeptide binding]; other site 316055003973 subunit L interaction residues [polypeptide binding]; other site 316055003974 putative proton transfer pathway, P1; other site 316055003975 putative proton transfer pathway, P2; other site 316055003976 Bacterial PH domain; Region: DUF304; pfam03703 316055003977 putative photosynthetic complex assembly protein; Region: photo_alph_chp1; TIGR03054 316055003978 Aerobic Cyclase System Fe-containing subunit (ACSF), ferritin-like diiron-binding domain; Region: ACSF; cd01047 316055003979 diiron binding motif [ion binding]; other site 316055003980 putative photosynthetic complex assembly protein 2; Region: photo_alph_chp2; TIGR03055 316055003981 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 316055003982 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 316055003983 substrate-cofactor binding pocket; other site 316055003984 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055003985 catalytic residue [active] 316055003986 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055003987 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055003988 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 316055003989 putative dimerization interface [polypeptide binding]; other site 316055003990 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 316055003991 Ribulose bisphosphate carboxylase large chain, Form I; Region: RuBisCO_large_I; cd08212 316055003992 homodimer interface [polypeptide binding]; other site 316055003993 active site 316055003994 heterodimer interface [polypeptide binding]; other site 316055003995 catalytic residue [active] 316055003996 metal binding site [ion binding]; metal-binding site 316055003997 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 316055003998 multimerization interface [polypeptide binding]; other site 316055003999 probable Rubsico expression protein CbbX; Region: cbbX_cfxQ; TIGR02880 316055004000 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055004001 Walker A motif; other site 316055004002 ATP binding site [chemical binding]; other site 316055004003 Walker B motif; other site 316055004004 arginine finger; other site 316055004005 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055004006 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055004007 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 316055004008 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 316055004009 homodimer interface [polypeptide binding]; other site 316055004010 substrate-cofactor binding pocket; other site 316055004011 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004012 catalytic residue [active] 316055004013 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 316055004014 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055004015 SlyX; Region: SlyX; pfam04102 316055004016 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 316055004017 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 316055004018 CsbD-like; Region: CsbD; pfam05532 316055004019 PAS fold; Region: PAS_4; pfam08448 316055004020 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 316055004021 putative active site [active] 316055004022 heme pocket [chemical binding]; other site 316055004023 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055004024 dimer interface [polypeptide binding]; other site 316055004025 phosphorylation site [posttranslational modification] 316055004026 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 316055004027 ATP binding site [chemical binding]; other site 316055004028 Mg2+ binding site [ion binding]; other site 316055004029 G-X-G motif; other site 316055004030 Response regulator receiver domain; Region: Response_reg; pfam00072 316055004031 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 316055004032 active site 316055004033 phosphorylation site [posttranslational modification] 316055004034 intermolecular recognition site; other site 316055004035 dimerization interface [polypeptide binding]; other site 316055004036 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 316055004037 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 316055004038 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055004039 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 316055004040 dimer interface [polypeptide binding]; other site 316055004041 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055004042 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 316055004043 E3 interaction surface; other site 316055004044 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055004045 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055004046 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055004047 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055004048 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 316055004049 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316055004050 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 316055004051 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 316055004052 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 316055004053 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 316055004054 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 316055004055 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 316055004056 Walker A/P-loop; other site 316055004057 ATP binding site [chemical binding]; other site 316055004058 Q-loop/lid; other site 316055004059 ABC transporter signature motif; other site 316055004060 Walker B; other site 316055004061 D-loop; other site 316055004062 H-loop/switch region; other site 316055004063 TOBE domain; Region: TOBE; pfam03459 316055004064 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 316055004065 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 316055004066 Walker A/P-loop; other site 316055004067 ATP binding site [chemical binding]; other site 316055004068 Q-loop/lid; other site 316055004069 ABC transporter signature motif; other site 316055004070 Walker B; other site 316055004071 D-loop; other site 316055004072 H-loop/switch region; other site 316055004073 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 316055004074 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055004075 dimer interface [polypeptide binding]; other site 316055004076 conserved gate region; other site 316055004077 putative PBP binding loops; other site 316055004078 ABC-ATPase subunit interface; other site 316055004079 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 316055004080 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055004081 dimer interface [polypeptide binding]; other site 316055004082 conserved gate region; other site 316055004083 putative PBP binding loops; other site 316055004084 ABC-ATPase subunit interface; other site 316055004085 Predicted small integral membrane protein (DUF2160); Region: DUF2160; pfam09928 316055004086 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 316055004087 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 316055004088 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 316055004089 FMN binding site [chemical binding]; other site 316055004090 active site 316055004091 substrate binding site [chemical binding]; other site 316055004092 catalytic residue [active] 316055004093 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055004094 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 316055004095 TM-ABC transporter signature motif; other site 316055004096 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055004097 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 316055004098 TM-ABC transporter signature motif; other site 316055004099 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055004100 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055004101 Walker A/P-loop; other site 316055004102 ATP binding site [chemical binding]; other site 316055004103 Q-loop/lid; other site 316055004104 ABC transporter signature motif; other site 316055004105 Walker B; other site 316055004106 D-loop; other site 316055004107 H-loop/switch region; other site 316055004108 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055004109 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055004110 Walker A/P-loop; other site 316055004111 ATP binding site [chemical binding]; other site 316055004112 Q-loop/lid; other site 316055004113 ABC transporter signature motif; other site 316055004114 Walker B; other site 316055004115 D-loop; other site 316055004116 H-loop/switch region; other site 316055004117 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055004118 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria; Region: PBP1_SBP_like_2; cd06328 316055004119 putative ligand binding site [chemical binding]; other site 316055004120 lytic murein transglycosylase; Region: MltB_2; TIGR02283 316055004121 murein hydrolase B; Provisional; Region: PRK10760; cl17906 316055004122 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055004123 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 316055004124 addiction module antitoxin, RelB/DinJ family; Region: RelB_DinJ; TIGR02384 316055004125 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055004126 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 316055004127 non-specific DNA binding site [nucleotide binding]; other site 316055004128 salt bridge; other site 316055004129 sequence-specific DNA binding site [nucleotide binding]; other site 316055004130 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 316055004131 Domain of unknown function (DUF955); Region: DUF955; pfam06114 316055004132 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 316055004133 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 316055004134 tetramer interface [polypeptide binding]; other site 316055004135 active site 316055004136 Mg2+/Mn2+ binding site [ion binding]; other site 316055004137 isocitrate lyase; Region: PLN02892 316055004138 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 316055004139 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 316055004140 putative active site [active] 316055004141 putative metal binding site [ion binding]; other site 316055004142 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_21; cd04680 316055004143 nudix motif; other site 316055004144 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 316055004145 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316055004146 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055004147 Coenzyme A binding pocket [chemical binding]; other site 316055004148 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 316055004149 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 316055004150 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 316055004151 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 316055004152 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 316055004153 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 316055004154 B1 nucleotide binding pocket [chemical binding]; other site 316055004155 B2 nucleotide binding pocket [chemical binding]; other site 316055004156 CAS motifs; other site 316055004157 active site 316055004158 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 316055004159 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 316055004160 active site 316055004161 Riboflavin kinase; Region: Flavokinase; smart00904 316055004162 maltose O-acetyltransferase; Provisional; Region: PRK10092 316055004163 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 316055004164 active site 316055004165 substrate binding site [chemical binding]; other site 316055004166 trimer interface [polypeptide binding]; other site 316055004167 CoA binding site [chemical binding]; other site 316055004168 RES domain; Region: RES; pfam08808 316055004169 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 316055004170 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 316055004171 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316055004172 active site 316055004173 HIGH motif; other site 316055004174 nucleotide binding site [chemical binding]; other site 316055004175 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 316055004176 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 316055004177 active site 316055004178 KMSKS motif; other site 316055004179 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 316055004180 tRNA binding surface [nucleotide binding]; other site 316055004181 anticodon binding site; other site 316055004182 lipoprotein signal peptidase; Provisional; Region: PRK14796 316055004183 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316055004184 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 316055004185 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316055004186 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316055004187 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 316055004188 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316055004189 hypothetical protein; Provisional; Region: PRK09256 316055004190 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 316055004191 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 316055004192 ATP binding site [chemical binding]; other site 316055004193 Mg2+ binding site [ion binding]; other site 316055004194 G-X-G motif; other site 316055004195 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 316055004196 ATP binding site [chemical binding]; other site 316055004197 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 316055004198 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 316055004199 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 316055004200 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 316055004201 homodimer interface [polypeptide binding]; other site 316055004202 substrate-cofactor binding pocket; other site 316055004203 catalytic residue [active] 316055004204 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 316055004205 MarR family; Region: MarR_2; pfam12802 316055004206 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 316055004207 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 316055004208 active site 316055004209 phosphorylation site [posttranslational modification] 316055004210 intermolecular recognition site; other site 316055004211 dimerization interface [polypeptide binding]; other site 316055004212 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055004213 DNA binding site [nucleotide binding] 316055004214 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055004215 HAMP domain; Region: HAMP; pfam00672 316055004216 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055004217 dimer interface [polypeptide binding]; other site 316055004218 phosphorylation site [posttranslational modification] 316055004219 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 316055004220 ATP binding site [chemical binding]; other site 316055004221 Mg2+ binding site [ion binding]; other site 316055004222 G-X-G motif; other site 316055004223 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 316055004224 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 316055004225 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 316055004226 riboflavin synthase subunit beta; Provisional; Region: PRK12419 316055004227 active site 316055004228 homopentamer interface [polypeptide binding]; other site 316055004229 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 316055004230 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 316055004231 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055004232 active site 316055004233 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 316055004234 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 316055004235 Uncharacterized conserved protein [Function unknown]; Region: COG1565 316055004236 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 316055004237 Membrane fusogenic activity; Region: BMFP; pfam04380 316055004238 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 316055004239 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 316055004240 5S rRNA interface [nucleotide binding]; other site 316055004241 CTC domain interface [polypeptide binding]; other site 316055004242 L16 interface [polypeptide binding]; other site 316055004243 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 316055004244 putative active site [active] 316055004245 catalytic residue [active] 316055004246 GTP-binding protein YchF; Reviewed; Region: PRK09601 316055004247 YchF GTPase; Region: YchF; cd01900 316055004248 G1 box; other site 316055004249 GTP/Mg2+ binding site [chemical binding]; other site 316055004250 Switch I region; other site 316055004251 G2 box; other site 316055004252 Switch II region; other site 316055004253 G3 box; other site 316055004254 G4 box; other site 316055004255 G5 box; other site 316055004256 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 316055004257 Domain of unknown function (DUF4282); Region: DUF4282; pfam14110 316055004258 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 316055004259 putative active site [active] 316055004260 putative catalytic site [active] 316055004261 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 316055004262 putative active site [active] 316055004263 putative catalytic site [active] 316055004264 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 316055004265 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 316055004266 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 316055004267 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055004268 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055004269 Walker A/P-loop; other site 316055004270 ATP binding site [chemical binding]; other site 316055004271 Q-loop/lid; other site 316055004272 ABC transporter signature motif; other site 316055004273 Walker B; other site 316055004274 D-loop; other site 316055004275 H-loop/switch region; other site 316055004276 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 316055004277 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 316055004278 NAD binding site [chemical binding]; other site 316055004279 homodimer interface [polypeptide binding]; other site 316055004280 active site 316055004281 substrate binding site [chemical binding]; other site 316055004282 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 316055004283 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 316055004284 putative active site [active] 316055004285 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 316055004286 active site 316055004287 motif I; other site 316055004288 motif II; other site 316055004289 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 316055004290 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 316055004291 putative active site [active] 316055004292 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 316055004293 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 316055004294 NADP binding site [chemical binding]; other site 316055004295 homopentamer interface [polypeptide binding]; other site 316055004296 substrate binding site [chemical binding]; other site 316055004297 active site 316055004298 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 316055004299 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 316055004300 putative ribose interaction site [chemical binding]; other site 316055004301 putative ADP binding site [chemical binding]; other site 316055004302 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 316055004303 active site 316055004304 nucleotide binding site [chemical binding]; other site 316055004305 HIGH motif; other site 316055004306 KMSKS motif; other site 316055004307 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055004308 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 316055004309 putative NAD(P) binding site [chemical binding]; other site 316055004310 active site 316055004311 putative substrate binding site [chemical binding]; other site 316055004312 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316055004313 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 316055004314 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 316055004315 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 316055004316 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 316055004317 inhibitor-cofactor binding pocket; inhibition site 316055004318 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004319 catalytic residue [active] 316055004320 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 316055004321 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 316055004322 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 316055004323 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 316055004324 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316055004325 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055004326 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055004327 Cytochrome C' Region: Cytochrom_C_2; pfam01322 316055004328 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 316055004329 Cytochrome c; Region: Cytochrom_C; pfam00034 316055004330 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 316055004331 dimer interface [polypeptide binding]; other site 316055004332 substrate binding site [chemical binding]; other site 316055004333 ATP binding site [chemical binding]; other site 316055004334 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 316055004335 S-adenosylmethionine binding site [chemical binding]; other site 316055004336 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316055004337 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 316055004338 putative active site [active] 316055004339 putative metal binding site [ion binding]; other site 316055004340 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055004341 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 316055004342 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 316055004343 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 316055004344 tetramer interface [polypeptide binding]; other site 316055004345 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004346 catalytic residue [active] 316055004347 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 316055004348 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 316055004349 active site 316055004350 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 316055004351 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 316055004352 Permease; Region: Permease; pfam02405 316055004353 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 316055004354 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 316055004355 Walker A/P-loop; other site 316055004356 ATP binding site [chemical binding]; other site 316055004357 Q-loop/lid; other site 316055004358 ABC transporter signature motif; other site 316055004359 Walker B; other site 316055004360 D-loop; other site 316055004361 H-loop/switch region; other site 316055004362 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 316055004363 mce related protein; Region: MCE; pfam02470 316055004364 transcriptional regulator ICP4; Provisional; Region: PHA03307 316055004365 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 316055004366 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 316055004367 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 316055004368 catalytic loop [active] 316055004369 iron binding site [ion binding]; other site 316055004370 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055004371 active site 316055004372 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 316055004373 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055004374 Predicted helicase [General function prediction only]; Region: COG4889 316055004375 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 316055004376 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055004377 dimer interface [polypeptide binding]; other site 316055004378 phosphorylation site [posttranslational modification] 316055004379 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 316055004380 ATP binding site [chemical binding]; other site 316055004381 Mg2+ binding site [ion binding]; other site 316055004382 G-X-G motif; other site 316055004383 CHASE domain; Region: CHASE; pfam03924 316055004384 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055004385 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055004386 metal binding site [ion binding]; metal-binding site 316055004387 active site 316055004388 I-site; other site 316055004389 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 316055004390 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 316055004391 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055004392 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055004393 metal binding site [ion binding]; metal-binding site 316055004394 active site 316055004395 I-site; other site 316055004396 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 316055004397 B12 binding domain; Region: B12-binding_2; pfam02607 316055004398 B12 binding domain; Region: B12-binding; pfam02310 316055004399 B12 binding site [chemical binding]; other site 316055004400 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 316055004401 active site 316055004402 oxyanion hole [active] 316055004403 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 316055004404 Predicted integral membrane protein [Function unknown]; Region: COG0392 316055004405 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 316055004406 dimerization interface [polypeptide binding]; other site 316055004407 metal binding site [ion binding]; metal-binding site 316055004408 Uncharacterized protein conserved in bacteria (DUF2200); Region: DUF2200; cl02047 316055004409 hypothetical protein; Provisional; Region: PRK12472 316055004410 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055004411 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 316055004412 Ligand Binding Site [chemical binding]; other site 316055004413 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; cd07040 316055004414 catalytic core [active] 316055004415 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 316055004416 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 316055004417 methionine sulfoxide reductase B; Provisional; Region: PRK00222 316055004418 SelR domain; Region: SelR; pfam01641 316055004419 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 316055004420 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 316055004421 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055004422 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 316055004423 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055004424 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055004425 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 316055004426 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 316055004427 dimer interface [polypeptide binding]; other site 316055004428 active site 316055004429 Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]; Region: HisB; COG0241 316055004430 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 316055004431 active site 316055004432 motif I; other site 316055004433 motif II; other site 316055004434 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 316055004435 active site 316055004436 intersubunit interactions; other site 316055004437 catalytic residue [active] 316055004438 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055004439 extended (e) SDRs; Region: SDR_e; cd08946 316055004440 NAD(P) binding site [chemical binding]; other site 316055004441 active site 316055004442 substrate binding site [chemical binding]; other site 316055004443 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055004444 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055004445 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055004446 NAD(P) binding site [chemical binding]; other site 316055004447 active site 316055004448 N-terminal domain of RfaE; Region: RfaE_N; cd02172 316055004449 putative active site [active] 316055004450 (T/H)XGH motif; other site 316055004451 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; Region: ribokinase_pfkB_like; cl00192 316055004452 substrate binding site [chemical binding]; other site 316055004453 ATP binding site [chemical binding]; other site 316055004454 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 316055004455 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316055004456 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 316055004457 nucleotide sugar dehydrogenase; Region: NDP-sugDHase; TIGR03026 316055004458 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316055004459 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 316055004460 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 316055004461 extended (e) SDRs; Region: SDR_e; cd08946 316055004462 NAD(P) binding site [chemical binding]; other site 316055004463 active site 316055004464 substrate binding site [chemical binding]; other site 316055004465 Methyltransferase domain; Region: Methyltransf_31; pfam13847 316055004466 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 316055004467 S-adenosylmethionine binding site [chemical binding]; other site 316055004468 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055004469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055004470 NAD(P) binding site [chemical binding]; other site 316055004471 active site 316055004472 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 316055004473 TPP-binding site [chemical binding]; other site 316055004474 dimer interface [polypeptide binding]; other site 316055004475 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 316055004476 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 316055004477 PYR/PP interface [polypeptide binding]; other site 316055004478 dimer interface [polypeptide binding]; other site 316055004479 TPP binding site [chemical binding]; other site 316055004480 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055004481 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 316055004482 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055004483 Methyltransferase domain; Region: Methyltransf_11; pfam08241 316055004484 S-adenosylmethionine binding site [chemical binding]; other site 316055004485 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 316055004486 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 316055004487 inhibitor-cofactor binding pocket; inhibition site 316055004488 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004489 catalytic residue [active] 316055004490 Methyltransferase domain; Region: Methyltransf_31; pfam13847 316055004491 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 316055004492 S-adenosylmethionine binding site [chemical binding]; other site 316055004493 flagellin; Provisional; Region: PRK14708 316055004494 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055004495 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055004496 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055004497 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 316055004498 TPR motif; other site 316055004499 binding surface 316055004500 TPR repeat; Region: TPR_11; pfam13414 316055004501 TPR repeat; Region: TPR_11; pfam13414 316055004502 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 316055004503 TPR motif; other site 316055004504 binding surface 316055004505 TPR repeat; Region: TPR_11; pfam13414 316055004506 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 316055004507 binding surface 316055004508 TPR motif; other site 316055004509 Tetratricopeptide repeat; Region: TPR_12; pfam13424 316055004510 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 316055004511 TPR motif; other site 316055004512 binding surface 316055004513 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 316055004514 flagellin; Provisional; Region: PRK14708 316055004515 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055004516 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055004517 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055004518 flagellar biosynthesis repressor FlbT; Reviewed; Region: flbT; PRK12791 316055004519 flagellar biosynthesis regulatory protein FlaF; Reviewed; Region: flaF; PRK12794 316055004520 chemotactic signal-response protein CheL; Provisional; Region: PRK12790 316055004521 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 316055004522 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 316055004523 flagellar assembly regulator FliX; Reviewed; Region: fliX; PRK12787 316055004524 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 316055004525 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055004526 dimerization interface [polypeptide binding]; other site 316055004527 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055004528 dimer interface [polypeptide binding]; other site 316055004529 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055004530 putative CheW interface [polypeptide binding]; other site 316055004531 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 316055004532 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 316055004533 SAF-like; Region: SAF_2; pfam13144 316055004534 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 316055004535 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 316055004536 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 316055004537 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316055004538 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055004539 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12689 316055004540 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 316055004541 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK12785 316055004542 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 316055004543 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 316055004544 Uncharacterized conserved protein [Function unknown]; Region: COG3334 316055004545 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 316055004546 putative substrate translocation pore; other site 316055004547 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055004548 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055004549 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055004550 dimerization interface [polypeptide binding]; other site 316055004551 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055004552 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055004553 dimer interface [polypeptide binding]; other site 316055004554 putative CheW interface [polypeptide binding]; other site 316055004555 Protein of unknown function (DUF1551); Region: DUF1551; pfam07585 316055004556 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 316055004557 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055004558 putative active site [active] 316055004559 heme pocket [chemical binding]; other site 316055004560 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 316055004561 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055004562 dimer interface [polypeptide binding]; other site 316055004563 phosphorylation site [posttranslational modification] 316055004564 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 316055004565 ATP binding site [chemical binding]; other site 316055004566 Mg2+ binding site [ion binding]; other site 316055004567 G-X-G motif; other site 316055004568 Response regulator receiver domain; Region: Response_reg; pfam00072 316055004569 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 316055004570 active site 316055004571 phosphorylation site [posttranslational modification] 316055004572 intermolecular recognition site; other site 316055004573 dimerization interface [polypeptide binding]; other site 316055004574 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 316055004575 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 316055004576 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 316055004577 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 316055004578 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00732 316055004579 flagellar biosynthesis protein FliQ; Reviewed; Region: fliQ; PRK06010 316055004580 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 316055004581 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 316055004582 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 316055004583 PAS domain; Region: PAS_9; pfam13426 316055004584 PAS fold; Region: PAS_4; pfam08448 316055004585 PAS fold; Region: PAS_4; pfam08448 316055004586 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055004587 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055004588 dimer interface [polypeptide binding]; other site 316055004589 phosphorylation site [posttranslational modification] 316055004590 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 316055004591 ATP binding site [chemical binding]; other site 316055004592 Mg2+ binding site [ion binding]; other site 316055004593 G-X-G motif; other site 316055004594 Response regulator receiver domain; Region: Response_reg; pfam00072 316055004595 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 316055004596 active site 316055004597 phosphorylation site [posttranslational modification] 316055004598 intermolecular recognition site; other site 316055004599 dimerization interface [polypeptide binding]; other site 316055004600 FRG domain; Region: FRG; pfam08867 316055004601 Tim44-like domain; Region: Tim44; pfam04280 316055004602 GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of...; Region: GST_N_Sigma_like; cd03039 316055004603 glutathione s-transferase; Provisional; Region: PTZ00057 316055004604 GSH binding site (G-site) [chemical binding]; other site 316055004605 C-terminal domain interface [polypeptide binding]; other site 316055004606 dimer interface [polypeptide binding]; other site 316055004607 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 316055004608 dimer interface [polypeptide binding]; other site 316055004609 N-terminal domain interface [polypeptide binding]; other site 316055004610 substrate binding pocket (H-site) [chemical binding]; other site 316055004611 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 316055004612 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055004613 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055004614 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055004615 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 316055004616 fumarate hydratase; Provisional; Region: PRK15389 316055004617 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 316055004618 Fumarase C-terminus; Region: Fumerase_C; pfam05683 316055004619 Protein of unknown function (DUF429); Region: DUF429; pfam04250 316055004620 Intracellular septation protein A; Region: IspA; cl01098 316055004621 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3670 316055004622 Retinal pigment epithelial membrane protein; Region: RPE65; pfam03055 316055004623 WHG domain; Region: WHG; pfam13305 316055004624 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 316055004625 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 316055004626 sequence-specific DNA binding site [nucleotide binding]; other site 316055004627 salt bridge; other site 316055004628 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 316055004629 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 316055004630 catalytic residues [active] 316055004631 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 316055004632 Caspase domain; Region: Peptidase_C14; pfam00656 316055004633 active site 316055004634 substrate pocket [chemical binding]; other site 316055004635 dimer interface [polypeptide binding]; other site 316055004636 proteolytic cleavage site; other site 316055004637 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 316055004638 PilZ domain; Region: PilZ; pfam07238 316055004639 P63C domain; Region: P63C; pfam10546 316055004640 recombinase A; Provisional; Region: recA; PRK09354 316055004641 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 316055004642 hexamer interface [polypeptide binding]; other site 316055004643 Walker A motif; other site 316055004644 ATP binding site [chemical binding]; other site 316055004645 Walker B motif; other site 316055004646 glycine dehydrogenase; Provisional; Region: PRK05367 316055004647 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 316055004648 tetramer interface [polypeptide binding]; other site 316055004649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004650 catalytic residue [active] 316055004651 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 316055004652 tetramer interface [polypeptide binding]; other site 316055004653 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055004654 catalytic residue [active] 316055004655 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 316055004656 lipoyl attachment site [posttranslational modification]; other site 316055004657 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 316055004658 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 316055004659 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 316055004660 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 316055004661 motif 1; other site 316055004662 active site 316055004663 motif 2; other site 316055004664 motif 3; other site 316055004665 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 316055004666 DHHA1 domain; Region: DHHA1; pfam02272 316055004667 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 316055004668 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055004669 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 316055004670 TrkA-N domain; Region: TrkA_N; pfam02254 316055004671 putative cation:proton antiport protein; Provisional; Region: PRK10669 316055004672 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 316055004673 TrkA-N domain; Region: TrkA_N; pfam02254 316055004674 isocitrate dehydrogenase; Validated; Region: PRK08299 316055004675 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 316055004676 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 316055004677 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316055004678 putative active site [active] 316055004679 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 316055004680 transcription elongation factor regulatory protein; Validated; Region: PRK06342 316055004681 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 316055004682 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 316055004683 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 316055004684 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 316055004685 ATP binding site [chemical binding]; other site 316055004686 active site 316055004687 substrate binding site [chemical binding]; other site 316055004688 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed; Region: PRK05974 316055004689 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 316055004690 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 316055004691 putative active site [active] 316055004692 catalytic triad [active] 316055004693 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 316055004694 CoenzymeA binding site [chemical binding]; other site 316055004695 subunit interaction site [polypeptide binding]; other site 316055004696 PHB binding site; other site 316055004697 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 316055004698 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 316055004699 dimerization interface [polypeptide binding]; other site 316055004700 ATP binding site [chemical binding]; other site 316055004701 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 316055004702 dimerization interface [polypeptide binding]; other site 316055004703 ATP binding site [chemical binding]; other site 316055004704 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055004705 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 316055004706 Domain of unknown function (DUF427); Region: DUF427; pfam04248 316055004707 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 316055004708 Bacterial low temperature requirement A protein (LtrA); Region: LtrA; cl01754 316055004709 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 316055004710 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 316055004711 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 316055004712 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 316055004713 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 316055004714 putative GSH binding site [chemical binding]; other site 316055004715 catalytic residues [active] 316055004716 Macro domain, 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 polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 316055004717 ADP-ribose binding site [chemical binding]; other site 316055004718 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055004719 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055004720 LssY C-terminus; Region: LssY_C; pfam14067 316055004721 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 316055004722 The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of...; Region: Delta12-FADS-like; cd03507 316055004723 putative di-iron ligands [ion binding]; other site 316055004724 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_17; cd08356 316055004725 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055004726 Histidine kinase; Region: HisKA_2; pfam07568 316055004727 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055004728 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 316055004729 ATP binding site [chemical binding]; other site 316055004730 Mg2+ binding site [ion binding]; other site 316055004731 G-X-G motif; other site 316055004732 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 316055004733 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 316055004734 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055004735 catalytic residue [active] 316055004736 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 316055004737 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 316055004738 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 316055004739 RNA binding surface [nucleotide binding]; other site 316055004740 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055004741 Coenzyme A binding pocket [chemical binding]; other site 316055004742 Cupin domain; Region: Cupin_2; pfam07883 316055004743 glutamate racemase; Provisional; Region: PRK00865 316055004744 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 316055004745 MOSC domain; Region: MOSC; pfam03473 316055004746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 316055004747 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4453 316055004748 adenylosuccinate lyase; Provisional; Region: PRK07492 316055004749 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 316055004750 tetramer interface [polypeptide binding]; other site 316055004751 active site 316055004752 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 316055004753 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 316055004754 substrate binding site [chemical binding]; other site 316055004755 hexamer interface [polypeptide binding]; other site 316055004756 metal binding site [ion binding]; metal-binding site 316055004757 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...; Region: nylC_like; cd02252 316055004758 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...; Region: nylC_like; cd02252 316055004759 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 316055004760 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 316055004761 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055004762 GIY-YIG motif/motif A; other site 316055004763 putative active site [active] 316055004764 putative metal binding site [ion binding]; other site 316055004765 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055004766 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 316055004767 dimerization interface [polypeptide binding]; other site 316055004768 ligand binding site [chemical binding]; other site 316055004769 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055004770 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055004771 Walker A/P-loop; other site 316055004772 ATP binding site [chemical binding]; other site 316055004773 Q-loop/lid; other site 316055004774 ABC transporter signature motif; other site 316055004775 Walker B; other site 316055004776 D-loop; other site 316055004777 H-loop/switch region; other site 316055004778 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055004779 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055004780 Walker A/P-loop; other site 316055004781 ATP binding site [chemical binding]; other site 316055004782 Q-loop/lid; other site 316055004783 ABC transporter signature motif; other site 316055004784 Walker B; other site 316055004785 D-loop; other site 316055004786 H-loop/switch region; other site 316055004787 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 316055004788 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 316055004789 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 316055004790 TM-ABC transporter signature motif; other site 316055004791 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055004792 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 316055004793 TM-ABC transporter signature motif; other site 316055004794 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 316055004795 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 316055004796 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 316055004797 putative hydrophobic ligand binding site [chemical binding]; other site 316055004798 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 316055004799 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 316055004800 catalytic loop [active] 316055004801 iron binding site [ion binding]; other site 316055004802 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316055004803 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 316055004804 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 316055004805 MoxR-like ATPases [General function prediction only]; Region: COG0714 316055004806 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055004807 Walker A motif; other site 316055004808 ATP binding site [chemical binding]; other site 316055004809 Walker B motif; other site 316055004810 arginine finger; other site 316055004811 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 316055004812 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 316055004813 metal ion-dependent adhesion site (MIDAS); other site 316055004814 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 316055004815 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 316055004816 XdhC Rossmann domain; Region: XdhC_C; pfam13478 316055004817 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 316055004818 putative MPT binding site; other site 316055004819 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 316055004820 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 316055004821 Ligand binding site; other site 316055004822 metal-binding site 316055004823 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055004824 Domain of unknown function (DUF4189); Region: DUF4189; pfam13827 316055004825 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055004826 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055004827 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055004828 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 316055004829 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055004830 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 316055004831 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055004832 Walker A/P-loop; other site 316055004833 ATP binding site [chemical binding]; other site 316055004834 Q-loop/lid; other site 316055004835 ABC transporter signature motif; other site 316055004836 Walker B; other site 316055004837 D-loop; other site 316055004838 H-loop/switch region; other site 316055004839 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 316055004840 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 316055004841 Sulfatase; Region: Sulfatase; cl17466 316055004842 Protein of unknown function, DUF488; Region: DUF488; pfam04343 316055004843 Protein of unknown function DUF72; Region: DUF72; pfam01904 316055004844 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 316055004845 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 316055004846 Ligand binding site; other site 316055004847 Putative Catalytic site; other site 316055004848 DXD motif; other site 316055004849 Predicted membrane protein [Function unknown]; Region: COG2246 316055004850 GtrA-like protein; Region: GtrA; pfam04138 316055004851 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 316055004852 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 316055004853 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055004854 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 316055004855 Ribokinase-like subgroup B. Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_B; cd01945 316055004856 substrate binding site [chemical binding]; other site 316055004857 ATP binding site [chemical binding]; other site 316055004858 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 316055004859 active site 316055004860 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055004861 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055004862 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055004863 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055004864 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055004865 multidrug efflux protein; Reviewed; Region: PRK09579 316055004866 Protein export membrane protein; Region: SecD_SecF; cl14618 316055004867 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 316055004868 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055004869 hydroxyglutarate oxidase; Provisional; Region: PRK11728 316055004870 PGAP1-like protein; Region: PGAP1; pfam07819 316055004871 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 316055004872 Phasin protein; Region: Phasin_2; cl11491 316055004873 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055004874 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055004875 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 316055004876 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 316055004877 bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and...; Region: arch_bact_SO_family_Moco; cd02109 316055004878 Moco binding site; other site 316055004879 metal coordination site [ion binding]; other site 316055004880 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 316055004881 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 316055004882 NAD binding site [chemical binding]; other site 316055004883 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 316055004884 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055004885 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055004886 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 316055004887 dimerization interface [polypeptide binding]; other site 316055004888 hypothetical protein; Provisional; Region: PRK05463 316055004889 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055004890 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_6; cd06340 316055004891 putative ligand binding site [chemical binding]; other site 316055004892 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 316055004893 TM-ABC transporter signature motif; other site 316055004894 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055004895 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 316055004896 TM-ABC transporter signature motif; other site 316055004897 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055004898 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055004899 Walker A/P-loop; other site 316055004900 ATP binding site [chemical binding]; other site 316055004901 Q-loop/lid; other site 316055004902 ABC transporter signature motif; other site 316055004903 Walker B; other site 316055004904 D-loop; other site 316055004905 H-loop/switch region; other site 316055004906 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055004907 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055004908 Walker A/P-loop; other site 316055004909 ATP binding site [chemical binding]; other site 316055004910 Q-loop/lid; other site 316055004911 ABC transporter signature motif; other site 316055004912 Walker B; other site 316055004913 D-loop; other site 316055004914 H-loop/switch region; other site 316055004915 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055004916 GIY-YIG motif/motif A; other site 316055004917 putative active site [active] 316055004918 putative metal binding site [ion binding]; other site 316055004919 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 316055004920 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055004921 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055004922 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055004923 acetyl-CoA acetyltransferase; Validated; Region: PRK08257 316055004924 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 316055004925 active site 316055004926 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055004927 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055004928 NAD(P) binding site [chemical binding]; other site 316055004929 active site 316055004930 enoyl-CoA hydratase; Provisional; Region: PRK05981 316055004931 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 316055004932 substrate binding site [chemical binding]; other site 316055004933 oxyanion hole (OAH) forming residues; other site 316055004934 trimer interface [polypeptide binding]; other site 316055004935 Phosphotransferase enzyme family; Region: APH; pfam01636 316055004936 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 316055004937 putative active site [active] 316055004938 putative substrate binding site [chemical binding]; other site 316055004939 ATP binding site [chemical binding]; other site 316055004940 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 316055004941 40S ribosomal protein S3; Provisional; Region: PTZ00084 316055004942 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 316055004943 catalytic triad [active] 316055004944 dimer interface [polypeptide binding]; other site 316055004945 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 316055004946 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 316055004947 acyl-activating enzyme (AAE) consensus motif; other site 316055004948 putative AMP binding site [chemical binding]; other site 316055004949 putative active site [active] 316055004950 putative CoA binding site [chemical binding]; other site 316055004951 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 316055004952 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 316055004953 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 316055004954 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055004955 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055004956 Walker A/P-loop; other site 316055004957 ATP binding site [chemical binding]; other site 316055004958 Q-loop/lid; other site 316055004959 ABC transporter signature motif; other site 316055004960 Walker B; other site 316055004961 D-loop; other site 316055004962 H-loop/switch region; other site 316055004963 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 316055004964 NADH dehydrogenase subunit B; Validated; Region: PRK06411 316055004965 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 316055004966 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 316055004967 NADH dehydrogenase subunit D; Validated; Region: PRK06075 316055004968 NADH dehydrogenase subunit E; Validated; Region: PRK07539 316055004969 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 316055004970 putative dimer interface [polypeptide binding]; other site 316055004971 [2Fe-2S] cluster binding site [ion binding]; other site 316055004972 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 316055004973 SLBB domain; Region: SLBB; pfam10531 316055004974 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 316055004975 NADH dehydrogenase subunit G; Validated; Region: PRK08166 316055004976 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 316055004977 catalytic loop [active] 316055004978 iron binding site [ion binding]; other site 316055004979 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 316055004980 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 316055004981 molybdopterin cofactor binding site; other site 316055004982 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 316055004983 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 316055004984 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 316055004985 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 316055004986 4Fe-4S binding domain; Region: Fer4; cl02805 316055004987 4Fe-4S binding domain; Region: Fer4; pfam00037 316055004988 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 316055004989 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 316055004990 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 316055004991 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055004992 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 316055004993 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055004994 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055004995 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 316055004996 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 316055004997 homodimer interface [polypeptide binding]; other site 316055004998 substrate-cofactor binding pocket; other site 316055004999 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055005000 catalytic residue [active] 316055005001 transcriptional regulator FixK; Provisional; Region: fixK; PRK09391 316055005002 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 316055005003 ligand binding site [chemical binding]; other site 316055005004 flexible hinge region; other site 316055005005 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 316055005006 putative switch regulator; other site 316055005007 non-specific DNA interactions [nucleotide binding]; other site 316055005008 DNA binding site [nucleotide binding] 316055005009 sequence specific DNA binding site [nucleotide binding]; other site 316055005010 putative cAMP binding site [chemical binding]; other site 316055005011 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 316055005012 active site 316055005013 phosphorylation site [posttranslational modification] 316055005014 intermolecular recognition site; other site 316055005015 dimerization interface [polypeptide binding]; other site 316055005016 response regulator FixJ; Provisional; Region: fixJ; PRK09390 316055005017 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 316055005018 active site 316055005019 phosphorylation site [posttranslational modification] 316055005020 intermolecular recognition site; other site 316055005021 dimerization interface [polypeptide binding]; other site 316055005022 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055005023 DNA binding residues [nucleotide binding] 316055005024 dimerization interface [polypeptide binding]; other site 316055005025 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 316055005026 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055005027 putative active site [active] 316055005028 heme pocket [chemical binding]; other site 316055005029 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 316055005030 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 316055005031 putative active site [active] 316055005032 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005033 dimer interface [polypeptide binding]; other site 316055005034 phosphorylation site [posttranslational modification] 316055005035 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 316055005036 ATP binding site [chemical binding]; other site 316055005037 Mg2+ binding site [ion binding]; other site 316055005038 G-X-G motif; other site 316055005039 FOG: CBS domain [General function prediction only]; Region: COG0517 316055005040 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 316055005041 BON domain; Region: BON; pfam04972 316055005042 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 316055005043 Ligand Binding Site [chemical binding]; other site 316055005044 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 316055005045 Ligand Binding Site [chemical binding]; other site 316055005046 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 316055005047 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 316055005048 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 316055005049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 316055005050 Predicted kinase [General function prediction only]; Region: COG0645 316055005051 FOG: CBS domain [General function prediction only]; Region: COG0517 316055005052 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 316055005053 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 316055005054 CoA binding domain; Region: CoA_binding_2; pfam13380 316055005055 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 316055005056 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 316055005057 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055005058 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055005059 anthranilate synthase component I, non-proteobacterial lineages; Region: trpE_most; TIGR00564 316055005060 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 316055005061 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 316055005062 Permease; Region: Permease; pfam02405 316055005063 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 316055005064 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 316055005065 Walker A/P-loop; other site 316055005066 ATP binding site [chemical binding]; other site 316055005067 Q-loop/lid; other site 316055005068 ABC transporter signature motif; other site 316055005069 Walker B; other site 316055005070 D-loop; other site 316055005071 H-loop/switch region; other site 316055005072 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 316055005073 mce related protein; Region: MCE; pfam02470 316055005074 Protein of unknown function (DUF330); Region: DUF330; cl01135 316055005075 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 316055005076 Cytochrome c; Region: Cytochrom_C; pfam00034 316055005077 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 316055005078 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055005079 ligand binding site [chemical binding]; other site 316055005080 flexible hinge region; other site 316055005081 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 316055005082 putative switch regulator; other site 316055005083 non-specific DNA interactions [nucleotide binding]; other site 316055005084 DNA binding site [nucleotide binding] 316055005085 sequence specific DNA binding site [nucleotide binding]; other site 316055005086 putative cAMP binding site [chemical binding]; other site 316055005087 Ion transport protein; Region: Ion_trans; pfam00520 316055005088 Ion channel; Region: Ion_trans_2; pfam07885 316055005089 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055005090 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 316055005091 ligand binding site [chemical binding]; other site 316055005092 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055005093 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 316055005094 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055005095 HWE histidine kinase; Region: HWE_HK; pfam07536 316055005096 RNA polymerase sigma factor; Provisional; Region: PRK12540 316055005097 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055005098 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055005099 DNA binding residues [nucleotide binding] 316055005100 two-component response regulator; Provisional; Region: PRK09191 316055005101 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 316055005102 active site 316055005103 phosphorylation site [posttranslational modification] 316055005104 intermolecular recognition site; other site 316055005105 dimerization interface [polypeptide binding]; other site 316055005106 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316055005107 Domain of unknown function DUF20; Region: UPF0118; pfam01594 316055005108 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055005109 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055005110 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 316055005111 malate synthase G; Provisional; Region: PRK02999 316055005112 active site 316055005113 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005114 dimer interface [polypeptide binding]; other site 316055005115 conserved gate region; other site 316055005116 putative PBP binding loops; other site 316055005117 ABC-ATPase subunit interface; other site 316055005118 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 316055005119 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005120 dimer interface [polypeptide binding]; other site 316055005121 conserved gate region; other site 316055005122 putative PBP binding loops; other site 316055005123 ABC-ATPase subunit interface; other site 316055005124 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 316055005125 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 316055005126 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 316055005127 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 316055005128 CysD dimerization site [polypeptide binding]; other site 316055005129 G1 box; other site 316055005130 putative GEF interaction site [polypeptide binding]; other site 316055005131 GTP/Mg2+ binding site [chemical binding]; other site 316055005132 Switch I region; other site 316055005133 G2 box; other site 316055005134 G3 box; other site 316055005135 Switch II region; other site 316055005136 G4 box; other site 316055005137 G5 box; other site 316055005138 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 316055005139 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 316055005140 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 316055005141 ligand-binding site [chemical binding]; other site 316055005142 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 316055005143 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 316055005144 Active Sites [active] 316055005145 siroheme synthase; Provisional; Region: cysG; PRK10637 316055005146 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 316055005147 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 316055005148 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 316055005149 active site 316055005150 SAM binding site [chemical binding]; other site 316055005151 homodimer interface [polypeptide binding]; other site 316055005152 Protein of unknown function (DUF2849); Region: DUF2849; pfam11011 316055005153 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 316055005154 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316055005155 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316055005156 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 316055005157 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 316055005158 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 316055005159 Active Sites [active] 316055005160 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 316055005161 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055005162 substrate binding pocket [chemical binding]; other site 316055005163 membrane-bound complex binding site; other site 316055005164 hinge residues; other site 316055005165 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 316055005166 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005167 dimer interface [polypeptide binding]; other site 316055005168 conserved gate region; other site 316055005169 putative PBP binding loops; other site 316055005170 ABC-ATPase subunit interface; other site 316055005171 sulfate transport protein; Provisional; Region: cysT; CHL00187 316055005172 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005173 dimer interface [polypeptide binding]; other site 316055005174 conserved gate region; other site 316055005175 putative PBP binding loops; other site 316055005176 ABC-ATPase subunit interface; other site 316055005177 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 316055005178 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 316055005179 Walker A/P-loop; other site 316055005180 ATP binding site [chemical binding]; other site 316055005181 Q-loop/lid; other site 316055005182 ABC transporter signature motif; other site 316055005183 Walker B; other site 316055005184 D-loop; other site 316055005185 H-loop/switch region; other site 316055005186 TOBE-like domain; Region: TOBE_3; pfam12857 316055005187 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 316055005188 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055005189 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 316055005190 NAD(P) binding site [chemical binding]; other site 316055005191 active site 316055005192 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 316055005193 Protein of unknown function (DUF497); Region: DUF497; pfam04365 316055005194 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055005195 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 316055005196 ligand binding site [chemical binding]; other site 316055005197 flexible hinge region; other site 316055005198 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055005199 Caspase domain; Region: Peptidase_C14; pfam00656 316055005200 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 316055005201 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055005202 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055005203 acyl-activating enzyme (AAE) consensus motif; other site 316055005204 putative AMP binding site [chemical binding]; other site 316055005205 putative active site [active] 316055005206 putative CoA binding site [chemical binding]; other site 316055005207 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 316055005208 short chain dehydrogenase; Provisional; Region: PRK07677 316055005209 NAD(P) binding site [chemical binding]; other site 316055005210 substrate binding site [chemical binding]; other site 316055005211 homotetramer interface [polypeptide binding]; other site 316055005212 active site 316055005213 homodimer interface [polypeptide binding]; other site 316055005214 enoyl-CoA hydratase; Provisional; Region: PRK07509 316055005215 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 316055005216 substrate binding site [chemical binding]; other site 316055005217 oxyanion hole (OAH) forming residues; other site 316055005218 trimer interface [polypeptide binding]; other site 316055005219 long-chain-fatty-acid--CoA ligase; Provisional; Region: PRK12406 316055005220 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055005221 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055005222 acyl-activating enzyme (AAE) consensus motif; other site 316055005223 putative AMP binding site [chemical binding]; other site 316055005224 putative active site [active] 316055005225 putative CoA binding site [chemical binding]; other site 316055005226 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 316055005227 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055005228 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 316055005229 putative dimerization interface [polypeptide binding]; other site 316055005230 Predicted membrane protein [Function unknown]; Region: COG2855 316055005231 Cache domain; Region: Cache_1; pfam02743 316055005232 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005233 dimerization interface [polypeptide binding]; other site 316055005234 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 316055005235 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 316055005236 putative active site [active] 316055005237 heme pocket [chemical binding]; other site 316055005238 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005239 dimer interface [polypeptide binding]; other site 316055005240 phosphorylation site [posttranslational modification] 316055005241 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 316055005242 ATP binding site [chemical binding]; other site 316055005243 Mg2+ binding site [ion binding]; other site 316055005244 G-X-G motif; other site 316055005245 Response regulator receiver domain; Region: Response_reg; pfam00072 316055005246 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 316055005247 active site 316055005248 phosphorylation site [posttranslational modification] 316055005249 intermolecular recognition site; other site 316055005250 dimerization interface [polypeptide binding]; other site 316055005251 PilZ domain; Region: PilZ; pfam07238 316055005252 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 316055005253 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 316055005254 Zn2+ binding site [ion binding]; other site 316055005255 Mg2+ binding site [ion binding]; other site 316055005256 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 316055005257 hydroxyglutarate oxidase; Provisional; Region: PRK11728 316055005258 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 316055005259 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 316055005260 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055005261 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055005262 ligand binding site [chemical binding]; other site 316055005263 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055005264 short chain dehydrogenase; Provisional; Region: PRK07791 316055005265 NAD(P) binding site [chemical binding]; other site 316055005266 active site 316055005267 thiolase; Provisional; Region: PRK06158 316055005268 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 316055005269 active site 316055005270 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]; Region: COG1545 316055005271 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 316055005272 DUF35 OB-fold domain; Region: DUF35; pfam01796 316055005273 amidase; Provisional; Region: PRK07056 316055005274 Amidase; Region: Amidase; cl11426 316055005275 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 316055005276 hypothetical protein; Provisional; Region: PRK08266 316055005277 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055005278 PYR/PP interface [polypeptide binding]; other site 316055005279 dimer interface [polypeptide binding]; other site 316055005280 TPP binding site [chemical binding]; other site 316055005281 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316055005282 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 316055005283 TPP-binding site [chemical binding]; other site 316055005284 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 316055005285 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055005286 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005287 dimerization interface [polypeptide binding]; other site 316055005288 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055005289 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005290 dimer interface [polypeptide binding]; other site 316055005291 putative CheW interface [polypeptide binding]; other site 316055005292 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 316055005293 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 316055005294 B12 binding domain; Region: B12-binding; pfam02310 316055005295 B12 binding site [chemical binding]; other site 316055005296 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 316055005297 Domain of unknown function (DUF4070); Region: DUF4070; pfam13282 316055005298 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 316055005299 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 316055005300 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 316055005301 active site lid residues [active] 316055005302 substrate binding pocket [chemical binding]; other site 316055005303 catalytic residues [active] 316055005304 substrate-Mg2+ binding site; other site 316055005305 aspartate-rich region 1; other site 316055005306 aspartate-rich region 2; other site 316055005307 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 316055005308 active site lid residues [active] 316055005309 substrate binding pocket [chemical binding]; other site 316055005310 catalytic residues [active] 316055005311 substrate-Mg2+ binding site; other site 316055005312 aspartate-rich region 1; other site 316055005313 aspartate-rich region 2; other site 316055005314 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055005315 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 316055005316 hypothetical protein; Provisional; Region: PRK07077 316055005317 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 316055005318 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 316055005319 FeS/SAM binding site; other site 316055005320 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 316055005321 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 316055005322 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 316055005323 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 316055005324 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 316055005325 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 316055005326 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 316055005327 inhibitor-cofactor binding pocket; inhibition site 316055005328 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055005329 catalytic residue [active] 316055005330 choline dehydrogenase; Validated; Region: PRK02106 316055005331 lycopene cyclase; Region: lycopene_cycl; TIGR01789 316055005332 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 316055005333 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 316055005334 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 316055005335 metal binding site [ion binding]; metal-binding site 316055005336 putative dimer interface [polypeptide binding]; other site 316055005337 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 316055005338 dimerization interface [polypeptide binding]; other site 316055005339 metal binding site [ion binding]; metal-binding site 316055005340 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 316055005341 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 316055005342 Fe-S cluster binding site [ion binding]; other site 316055005343 active site 316055005344 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 316055005345 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 316055005346 FeS/SAM binding site; other site 316055005347 Uncharacterized conserved protein [Function unknown]; Region: COG4544 316055005348 DNA Polymerase Y-family; Region: PolY_like; cd03468 316055005349 active site 316055005350 DNA binding site [nucleotide binding] 316055005351 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 316055005352 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 316055005353 putative active site [active] 316055005354 putative PHP Thumb interface [polypeptide binding]; other site 316055005355 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 316055005356 generic binding surface I; other site 316055005357 generic binding surface II; other site 316055005358 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055005359 Coenzyme A binding pocket [chemical binding]; other site 316055005360 Protein of unknown function, DUF399; Region: DUF399; pfam04187 316055005361 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 316055005362 PAS fold; Region: PAS_3; pfam08447 316055005363 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005364 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005365 metal binding site [ion binding]; metal-binding site 316055005366 active site 316055005367 I-site; other site 316055005368 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 316055005369 enoyl-CoA hydratase; Provisional; Region: PRK05862 316055005370 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 316055005371 substrate binding site [chemical binding]; other site 316055005372 oxyanion hole (OAH) forming residues; other site 316055005373 trimer interface [polypeptide binding]; other site 316055005374 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055005375 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005376 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005377 metal binding site [ion binding]; metal-binding site 316055005378 active site 316055005379 I-site; other site 316055005380 RNA polymerase sigma factor; Provisional; Region: PRK12515 316055005381 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055005382 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055005383 DNA binding residues [nucleotide binding] 316055005384 TIGR03809 family protein; Region: TIGR03809 316055005385 twin-arg-translocated uncharacterized repeat protein; Region: RR_plus_rpt_1; TIGR03808 316055005386 putative cofactor-binding repeat; Region: RR_fam_repeat; TIGR03807 316055005387 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 316055005388 putative substrate binding pocket [chemical binding]; other site 316055005389 AC domain interface; other site 316055005390 catalytic triad [active] 316055005391 AB domain interface; other site 316055005392 interchain disulfide; other site 316055005393 membrane ATPase/protein kinase; Provisional; Region: PRK09435 316055005394 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 316055005395 Walker A; other site 316055005396 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 316055005397 Protein of unknown function DUF86; Region: DUF86; cl01031 316055005398 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 316055005399 active site 316055005400 NTP binding site [chemical binding]; other site 316055005401 metal binding triad [ion binding]; metal-binding site 316055005402 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 316055005403 putative active site [active] 316055005404 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 316055005405 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 316055005406 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 316055005407 active site 316055005408 substrate binding site [chemical binding]; other site 316055005409 coenzyme B12 binding site [chemical binding]; other site 316055005410 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 316055005411 B12 binding site [chemical binding]; other site 316055005412 cobalt ligand [ion binding]; other site 316055005413 Uncharacterized conserved protein [Function unknown]; Region: COG3791 316055005414 methylmalonyl-CoA mutase, heterodimeric type, beta chain; Region: mmCoA_mut_beta; TIGR00642 316055005415 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 316055005416 heterodimer interface [polypeptide binding]; other site 316055005417 substrate interaction site [chemical binding]; other site 316055005418 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 316055005419 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 316055005420 catalytic center binding site [active] 316055005421 ATP binding site [chemical binding]; other site 316055005422 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 316055005423 homooctamer interface [polypeptide binding]; other site 316055005424 active site 316055005425 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 316055005426 dihydropteroate synthase; Region: DHPS; TIGR01496 316055005427 substrate binding pocket [chemical binding]; other site 316055005428 dimer interface [polypeptide binding]; other site 316055005429 inhibitor binding site; inhibition site 316055005430 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 316055005431 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 316055005432 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 316055005433 Walker A motif; other site 316055005434 ATP binding site [chemical binding]; other site 316055005435 Zonular occludens toxin (Zot); Region: Zot; cl17485 316055005436 hypothetical protein; Validated; Region: PRK09104 316055005437 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 316055005438 metal binding site [ion binding]; metal-binding site 316055005439 putative dimer interface [polypeptide binding]; other site 316055005440 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 316055005441 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005442 dimerization interface [polypeptide binding]; other site 316055005443 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005444 dimer interface [polypeptide binding]; other site 316055005445 putative CheW interface [polypeptide binding]; other site 316055005446 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055005447 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005448 dimer interface [polypeptide binding]; other site 316055005449 putative CheW interface [polypeptide binding]; other site 316055005450 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 316055005451 beta-lactamase TEM; Provisional; Region: PRK15442 316055005452 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 316055005453 Predicted transcriptional regulator [Transcription]; Region: COG4957 316055005454 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 316055005455 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 316055005456 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 316055005457 putative active site [active] 316055005458 heme pocket [chemical binding]; other site 316055005459 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005460 dimer interface [polypeptide binding]; other site 316055005461 phosphorylation site [posttranslational modification] 316055005462 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 316055005463 ATP binding site [chemical binding]; other site 316055005464 Mg2+ binding site [ion binding]; other site 316055005465 G-X-G motif; other site 316055005466 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055005467 Protein of unknown function (DUF1491); Region: DUF1491; pfam07372 316055005468 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055005469 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 316055005470 Predicted integral membrane protein [Function unknown]; Region: COG5436 316055005471 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 316055005472 Transglycosylase; Region: Transgly; pfam00912 316055005473 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 316055005474 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 316055005475 hypothetical protein; Provisional; Region: PRK05170 316055005476 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 316055005477 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055005478 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005479 dimer interface [polypeptide binding]; other site 316055005480 putative CheW interface [polypeptide binding]; other site 316055005481 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005482 dimerization interface [polypeptide binding]; other site 316055005483 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005484 dimer interface [polypeptide binding]; other site 316055005485 putative CheW interface [polypeptide binding]; other site 316055005486 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055005487 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005488 dimerization interface [polypeptide binding]; other site 316055005489 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005490 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055005491 dimer interface [polypeptide binding]; other site 316055005492 putative CheW interface [polypeptide binding]; other site 316055005493 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 316055005494 PAS fold; Region: PAS_3; pfam08447 316055005495 putative active site [active] 316055005496 heme pocket [chemical binding]; other site 316055005497 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 316055005498 heme pocket [chemical binding]; other site 316055005499 PAS fold; Region: PAS_3; pfam08447 316055005500 putative active site [active] 316055005501 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316055005502 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055005503 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055005504 HAMP domain; Region: HAMP; pfam00672 316055005505 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005506 dimer interface [polypeptide binding]; other site 316055005507 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055005508 putative CheW interface [polypeptide binding]; other site 316055005509 Uncharacterized conserved protein [Function unknown]; Region: COG5323 316055005510 Terminase-like family; Region: Terminase_6; pfam03237 316055005511 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055005512 GIY-YIG motif/motif A; other site 316055005513 putative active site [active] 316055005514 putative metal binding site [ion binding]; other site 316055005515 Phage-related protein [Function unknown]; Region: COG4695 316055005516 Phage portal protein; Region: Phage_portal; pfam04860 316055005517 PilZ domain; Region: PilZ; pfam07238 316055005518 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 316055005519 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 316055005520 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 316055005521 Predicted phage phi-C31 gp36 major capsid-like protein [General function prediction only]; Region: COG4653 316055005522 Phage capsid family; Region: Phage_capsid; pfam05065 316055005523 Domain of unknown function (DUF2019); Region: DUF2019; pfam09450 316055005524 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 triad...; Region: Tryp_SPc; cl00149 316055005525 active site 316055005526 substrate binding sites [chemical binding]; other site 316055005527 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 316055005528 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 316055005529 oligomerization interface [polypeptide binding]; other site 316055005530 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 316055005531 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 316055005532 Phage major tail protein 2; Region: Phage_tail_2; cl11463 316055005533 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 316055005534 phage conserved hypothetical protein; Region: phage_TIGR02216 316055005535 Phage-related minor tail protein [Function unknown]; Region: COG5281 316055005536 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 316055005537 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 316055005538 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 316055005539 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 316055005540 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 316055005541 putative phage cell wall peptidase, NlpC/P60 family; Region: phage_NlpC_fam; TIGR02219 316055005542 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 316055005543 Putative phage tail protein; Region: Phage-tail_3; pfam13550 316055005544 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 316055005545 Predicted chitinase [General function prediction only]; Region: COG3179 316055005546 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055005547 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 316055005548 active site 316055005549 phosphorylation site [posttranslational modification] 316055005550 intermolecular recognition site; other site 316055005551 dimerization interface [polypeptide binding]; other site 316055005552 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055005553 DNA binding site [nucleotide binding] 316055005554 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055005555 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055005556 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 316055005557 ATP binding site [chemical binding]; other site 316055005558 Mg2+ binding site [ion binding]; other site 316055005559 G-X-G motif; other site 316055005560 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 316055005561 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 316055005562 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 316055005563 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 316055005564 binding surface 316055005565 TPR motif; other site 316055005566 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 316055005567 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 316055005568 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 316055005569 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 316055005570 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 316055005571 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 316055005572 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 316055005573 diiron binding motif [ion binding]; other site 316055005574 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 316055005575 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 316055005576 catalytic loop [active] 316055005577 iron binding site [ion binding]; other site 316055005578 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 316055005579 diiron binding motif [ion binding]; other site 316055005580 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 316055005581 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055005582 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055005583 protein binding site [polypeptide binding]; other site 316055005584 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055005585 protein binding site [polypeptide binding]; other site 316055005586 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055005587 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 316055005588 active site 316055005589 phosphorylation site [posttranslational modification] 316055005590 intermolecular recognition site; other site 316055005591 dimerization interface [polypeptide binding]; other site 316055005592 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055005593 DNA binding site [nucleotide binding] 316055005594 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005595 dimerization interface [polypeptide binding]; other site 316055005596 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005597 dimer interface [polypeptide binding]; other site 316055005598 putative CheW interface [polypeptide binding]; other site 316055005599 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055005600 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005601 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005602 metal binding site [ion binding]; metal-binding site 316055005603 active site 316055005604 I-site; other site 316055005605 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005606 dimerization interface [polypeptide binding]; other site 316055005607 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005608 dimer interface [polypeptide binding]; other site 316055005609 phosphorylation site [posttranslational modification] 316055005610 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 316055005611 ATP binding site [chemical binding]; other site 316055005612 Mg2+ binding site [ion binding]; other site 316055005613 G-X-G motif; other site 316055005614 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 316055005615 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316055005616 metal binding triad; other site 316055005617 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316055005618 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316055005619 metal binding triad; other site 316055005620 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316055005621 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 316055005622 RNA polymerase sigma factor; Provisional; Region: PRK12512 316055005623 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055005624 Predicted integral membrane protein [Function unknown]; Region: COG5572 316055005625 hypothetical protein; Provisional; Region: PRK05409 316055005626 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 316055005627 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 316055005628 PAS fold; Region: PAS_3; pfam08447 316055005629 putative active site [active] 316055005630 heme pocket [chemical binding]; other site 316055005631 PAS fold; Region: PAS_7; pfam12860 316055005632 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055005633 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005634 dimer interface [polypeptide binding]; other site 316055005635 phosphorylation site [posttranslational modification] 316055005636 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 316055005637 ATP binding site [chemical binding]; other site 316055005638 Mg2+ binding site [ion binding]; other site 316055005639 G-X-G motif; other site 316055005640 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 316055005641 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 316055005642 Cation efflux family; Region: Cation_efflux; cl00316 316055005643 Cation efflux family; Region: Cation_efflux; cl00316 316055005644 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 316055005645 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 316055005646 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 316055005647 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 316055005648 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 316055005649 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 316055005650 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 316055005651 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 316055005652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 316055005653 formyl-coenzyme A transferase; Provisional; Region: PRK05398 316055005654 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055005655 Transcriptional regulators [Transcription]; Region: GntR; COG1802 316055005656 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316055005657 DNA-binding site [nucleotide binding]; DNA binding site 316055005658 FCD domain; Region: FCD; pfam07729 316055005659 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 316055005660 potassium uptake protein; Region: kup; TIGR00794 316055005661 Cysteine rich repeat; Region: Cys_rich_FGFR; pfam00839 316055005662 MauM/NapG family ferredoxin-type protein; Region: mauM_napG; TIGR00397 316055005663 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055005664 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 316055005665 active site 316055005666 phosphorylation site [posttranslational modification] 316055005667 intermolecular recognition site; other site 316055005668 dimerization interface [polypeptide binding]; other site 316055005669 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055005670 DNA binding site [nucleotide binding] 316055005671 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 316055005672 ATP binding site [chemical binding]; other site 316055005673 Mg2+ binding site [ion binding]; other site 316055005674 G-X-G motif; other site 316055005675 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 316055005676 IHF dimer interface [polypeptide binding]; other site 316055005677 IHF - DNA interface [nucleotide binding]; other site 316055005678 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 316055005679 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 316055005680 cobalt transport protein CbiM; Validated; Region: PRK06265 316055005681 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 316055005682 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 316055005683 nickel responsive regulator; Provisional; Region: PRK02967 316055005684 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 316055005685 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 316055005686 Copper resistance protein D; Region: CopD; cl00563 316055005687 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 316055005688 oxyanion hole (OAH) forming residues; other site 316055005689 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 316055005690 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 316055005691 FMN binding site [chemical binding]; other site 316055005692 active site 316055005693 catalytic residues [active] 316055005694 substrate binding site [chemical binding]; other site 316055005695 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 316055005696 catalytic motif [active] 316055005697 Catalytic residue [active] 316055005698 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055005699 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055005700 dimer interface [polypeptide binding]; other site 316055005701 phosphorylation site [posttranslational modification] 316055005702 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 316055005703 ATP binding site [chemical binding]; other site 316055005704 Mg2+ binding site [ion binding]; other site 316055005705 G-X-G motif; other site 316055005706 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 316055005707 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 316055005708 Domain of unknown function DUF59; Region: DUF59; pfam01883 316055005709 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 316055005710 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 316055005711 Walker A motif; other site 316055005712 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 316055005713 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 316055005714 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 316055005715 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 316055005716 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 316055005717 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 316055005718 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 316055005719 FeS/SAM binding site; other site 316055005720 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 316055005721 phosphoglycolate phosphatase; Provisional; Region: PRK13222 316055005722 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 316055005723 motif II; other site 316055005724 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 316055005725 tetramer (dimer of dimers) interface [polypeptide binding]; other site 316055005726 active site 316055005727 dimer interface [polypeptide binding]; other site 316055005728 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 316055005729 glutathione reductase; Validated; Region: PRK06116 316055005730 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055005731 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055005732 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 316055005733 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 316055005734 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 316055005735 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 316055005736 NAD synthetase; Provisional; Region: PRK13981 316055005737 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 316055005738 multimer interface [polypeptide binding]; other site 316055005739 active site 316055005740 catalytic triad [active] 316055005741 protein interface 1 [polypeptide binding]; other site 316055005742 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 316055005743 homodimer interface [polypeptide binding]; other site 316055005744 NAD binding pocket [chemical binding]; other site 316055005745 ATP binding pocket [chemical binding]; other site 316055005746 Mg binding site [ion binding]; other site 316055005747 active-site loop [active] 316055005748 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 316055005749 oligomeric interface; other site 316055005750 putative active site [active] 316055005751 homodimer interface [polypeptide binding]; other site 316055005752 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 316055005753 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 316055005754 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 316055005755 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 316055005756 active site 316055005757 HIGH motif; other site 316055005758 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 316055005759 KMSKS motif; other site 316055005760 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 316055005761 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 316055005762 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055005763 Coenzyme A binding pocket [chemical binding]; other site 316055005764 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 316055005765 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 316055005766 active site 316055005767 catalytic residues [active] 316055005768 metal binding site [ion binding]; metal-binding site 316055005769 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 316055005770 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 316055005771 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055005772 hypothetical protein; Provisional; Region: PRK12474 316055005773 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055005774 PYR/PP interface [polypeptide binding]; other site 316055005775 dimer interface [polypeptide binding]; other site 316055005776 TPP binding site [chemical binding]; other site 316055005777 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 316055005778 TPP-binding site [chemical binding]; other site 316055005779 dimer interface [polypeptide binding]; other site 316055005780 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 316055005781 FAD binding domain; Region: FAD_binding_4; pfam01565 316055005782 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 316055005783 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055005784 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 316055005785 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 316055005786 Walker A/P-loop; other site 316055005787 ATP binding site [chemical binding]; other site 316055005788 Q-loop/lid; other site 316055005789 ABC transporter signature motif; other site 316055005790 Walker B; other site 316055005791 D-loop; other site 316055005792 H-loop/switch region; other site 316055005793 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 316055005794 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 316055005795 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 316055005796 CDP-alcohol phosphatidyltransferase 2; Region: CDP-OH_P_tran_2; pfam08009 316055005797 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316055005798 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 316055005799 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 316055005800 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 316055005801 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055005802 ligand binding site [chemical binding]; other site 316055005803 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 316055005804 potassium uptake protein; Region: kup; TIGR00794 316055005805 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 316055005806 active site residue [active] 316055005807 hypothetical protein; Provisional; Region: PRK08912 316055005808 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 316055005809 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055005810 homodimer interface [polypeptide binding]; other site 316055005811 catalytic residue [active] 316055005812 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 316055005813 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 316055005814 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 316055005815 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 316055005816 putative acyl-acceptor binding pocket; other site 316055005817 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 316055005818 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 316055005819 NAD(P) binding site [chemical binding]; other site 316055005820 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06501 316055005821 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 316055005822 dimer interface [polypeptide binding]; other site 316055005823 active site 316055005824 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06519 316055005825 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 316055005826 active site 316055005827 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 316055005828 acyl carrier protein; Provisional; Region: PRK06508 316055005829 MgtC family; Region: MgtC; pfam02308 316055005830 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 316055005831 PA26 p53-induced protein (sestrin); Region: PA26; pfam04636 316055005832 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 316055005833 HerA helicase [Replication, recombination, and repair]; Region: COG0433 316055005834 Domain of unknown function DUF87; Region: DUF87; pfam01935 316055005835 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 316055005836 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055005837 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 316055005838 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 316055005839 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055005840 Walker A motif; other site 316055005841 ATP binding site [chemical binding]; other site 316055005842 Walker B motif; other site 316055005843 arginine finger; other site 316055005844 PAS domain S-box; Region: sensory_box; TIGR00229 316055005845 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 316055005846 putative active site [active] 316055005847 heme pocket [chemical binding]; other site 316055005848 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005849 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005850 metal binding site [ion binding]; metal-binding site 316055005851 active site 316055005852 I-site; other site 316055005853 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 316055005854 Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a...; Region: Polysulfide_ST; cd01447 316055005855 active site 316055005856 catalytic residue [active] 316055005857 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 316055005858 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 316055005859 active site residue [active] 316055005860 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 316055005861 active site residue [active] 316055005862 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055005863 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055005864 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 316055005865 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055005866 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055005867 ABC transporter; Region: ABC_tran_2; pfam12848 316055005868 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055005869 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 316055005870 putative active site [active] 316055005871 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 316055005872 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 316055005873 Protein of unknown function (DUF3680); Region: DUF3680; pfam12441 316055005874 Protein of unknown function (DUF497); Region: DUF497; pfam04365 316055005875 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 316055005876 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 316055005877 S-adenosylmethionine binding site [chemical binding]; other site 316055005878 hypothetical protein; Provisional; Region: PRK05208 316055005879 Predicted sugar isomerase [Cell envelope biogenesis, outer membrane]; Region: COG4952; cl17900 316055005880 lytic murein transglycosylase; Region: MltB_2; TIGR02283 316055005881 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055005882 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055005883 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055005884 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 316055005885 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005886 dimer interface [polypeptide binding]; other site 316055005887 conserved gate region; other site 316055005888 ABC-ATPase subunit interface; other site 316055005889 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 316055005890 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055005891 dimer interface [polypeptide binding]; other site 316055005892 conserved gate region; other site 316055005893 ABC-ATPase subunit interface; other site 316055005894 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 316055005895 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 316055005896 Walker A/P-loop; other site 316055005897 ATP binding site [chemical binding]; other site 316055005898 Q-loop/lid; other site 316055005899 ABC transporter signature motif; other site 316055005900 Walker B; other site 316055005901 D-loop; other site 316055005902 H-loop/switch region; other site 316055005903 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 316055005904 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 316055005905 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 316055005906 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 316055005907 heme binding site [chemical binding]; other site 316055005908 ferroxidase pore; other site 316055005909 ferroxidase diiron center [ion binding]; other site 316055005910 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055005911 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055005912 dimer interface [polypeptide binding]; other site 316055005913 putative CheW interface [polypeptide binding]; other site 316055005914 Predicted membrane protein [Function unknown]; Region: COG4270 316055005915 Protein of unknown function (DUF2380); Region: DUF3280; pfam11684 316055005916 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005917 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005918 metal binding site [ion binding]; metal-binding site 316055005919 active site 316055005920 I-site; other site 316055005921 Hemerythrin; Region: Hemerythrin; cd12107 316055005922 Fe binding site [ion binding]; other site 316055005923 Protein of unknown function (DUF2283); Region: DUF2283; pfam10049 316055005924 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 316055005925 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 316055005926 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 316055005927 ThiC-associated domain; Region: ThiC-associated; pfam13667 316055005928 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 316055005929 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 316055005930 thiamine phosphate binding site [chemical binding]; other site 316055005931 active site 316055005932 pyrophosphate binding site [ion binding]; other site 316055005933 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 316055005934 ThiS interaction site; other site 316055005935 putative active site [active] 316055005936 tetramer interface [polypeptide binding]; other site 316055005937 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 316055005938 thiS-thiF/thiG interaction site; other site 316055005939 hydroxyglutarate oxidase; Provisional; Region: PRK11728 316055005940 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 316055005941 PRC-barrel domain; Region: PRC; pfam05239 316055005942 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 316055005943 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055005944 Domain of unknown function (DUF4403); Region: DUF4403; pfam14356 316055005945 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055005946 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055005947 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 316055005948 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 316055005949 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 316055005950 active site 316055005951 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055005952 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055005953 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 316055005954 putative effector binding pocket; other site 316055005955 putative dimerization interface [polypeptide binding]; other site 316055005956 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 316055005957 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 316055005958 active site 316055005959 catalytic tetrad [active] 316055005960 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 316055005961 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 316055005962 putative NAD(P) binding site [chemical binding]; other site 316055005963 putative substrate binding site [chemical binding]; other site 316055005964 catalytic Zn binding site [ion binding]; other site 316055005965 structural Zn binding site [ion binding]; other site 316055005966 dimer interface [polypeptide binding]; other site 316055005967 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055005968 MarR family; Region: MarR_2; pfam12802 316055005969 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055005970 dimerization interface [polypeptide binding]; other site 316055005971 PAS fold; Region: PAS_7; pfam12860 316055005972 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055005973 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055005974 metal binding site [ion binding]; metal-binding site 316055005975 active site 316055005976 I-site; other site 316055005977 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 316055005978 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 316055005979 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 316055005980 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055005981 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055005982 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 316055005983 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 316055005984 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055005985 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055005986 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 316055005987 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 316055005988 putative substrate translocation pore; other site 316055005989 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 316055005990 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 316055005991 Methyltransferase domain; Region: Methyltransf_31; pfam13847 316055005992 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 316055005993 S-adenosylmethionine binding site [chemical binding]; other site 316055005994 Cupin; Region: Cupin_6; pfam12852 316055005995 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055005996 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316055005997 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055005998 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 316055005999 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 316055006000 amidase catalytic site [active] 316055006001 Zn binding residues [ion binding]; other site 316055006002 substrate binding site [chemical binding]; other site 316055006003 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055006004 MraW methylase family; Region: Methyltransf_5; cl17771 316055006005 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 316055006006 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 316055006007 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 316055006008 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 316055006009 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 316055006010 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 316055006011 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316055006012 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316055006013 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316055006014 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 316055006015 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316055006016 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316055006017 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316055006018 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 316055006019 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 316055006020 Mg++ binding site [ion binding]; other site 316055006021 putative catalytic motif [active] 316055006022 putative substrate binding site [chemical binding]; other site 316055006023 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 316055006024 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 316055006025 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316055006026 cell division protein FtsW; Region: ftsW; TIGR02614 316055006027 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 316055006028 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 316055006029 active site 316055006030 homodimer interface [polypeptide binding]; other site 316055006031 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 316055006032 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316055006033 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316055006034 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316055006035 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055006036 GIY-YIG motif/motif A; other site 316055006037 putative active site [active] 316055006038 putative metal binding site [ion binding]; other site 316055006039 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 316055006040 FAD binding domain; Region: FAD_binding_4; pfam01565 316055006041 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 316055006042 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 316055006043 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 316055006044 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 316055006045 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 316055006046 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 316055006047 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055006048 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 316055006049 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 316055006050 Cell division protein FtsQ; Region: FtsQ; pfam03799 316055006051 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 316055006052 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 316055006053 nucleotide binding site [chemical binding]; other site 316055006054 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 316055006055 Cell division protein FtsA; Region: FtsA; pfam14450 316055006056 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 316055006057 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 316055006058 nucleotide binding site [chemical binding]; other site 316055006059 SulA interaction site; other site 316055006060 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 316055006061 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 316055006062 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 316055006063 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 316055006064 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 316055006065 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 316055006066 Walker A/P-loop; other site 316055006067 ATP binding site [chemical binding]; other site 316055006068 Q-loop/lid; other site 316055006069 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 316055006070 ABC transporter signature motif; other site 316055006071 Walker B; other site 316055006072 D-loop; other site 316055006073 H-loop/switch region; other site 316055006074 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055006075 GIY-YIG motif/motif A; other site 316055006076 putative active site [active] 316055006077 putative metal binding site [ion binding]; other site 316055006078 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 316055006079 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 316055006080 nucleotide binding pocket [chemical binding]; other site 316055006081 K-X-D-G motif; other site 316055006082 catalytic site [active] 316055006083 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 316055006084 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 316055006085 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 316055006086 Dimer interface [polypeptide binding]; other site 316055006087 BRCT sequence motif; other site 316055006088 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055006089 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 316055006090 putative substrate translocation pore; other site 316055006091 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 316055006092 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 316055006093 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 316055006094 active site 316055006095 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 316055006096 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055006097 Fic/DOC family; Region: Fic; pfam02661 316055006098 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 316055006099 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055006100 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 316055006101 S-adenosylmethionine binding site [chemical binding]; other site 316055006102 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055006103 ABC-2 type transporter; Region: ABC2_membrane; cl17235 316055006104 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316055006105 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 316055006106 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055006107 Walker A/P-loop; other site 316055006108 ATP binding site [chemical binding]; other site 316055006109 Q-loop/lid; other site 316055006110 ABC transporter signature motif; other site 316055006111 Walker B; other site 316055006112 D-loop; other site 316055006113 H-loop/switch region; other site 316055006114 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 316055006115 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 316055006116 YcfA-like protein; Region: YcfA; pfam07927 316055006117 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 316055006118 Part of AAA domain; Region: AAA_19; pfam13245 316055006119 Family description; Region: UvrD_C_2; pfam13538 316055006120 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055006121 active site 316055006122 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 316055006123 FAD binding domain; Region: FAD_binding_4; pfam01565 316055006124 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 316055006125 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 316055006126 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 316055006127 fumarate hydratase; Reviewed; Region: fumC; PRK00485 316055006128 Class II fumarases; Region: Fumarase_classII; cd01362 316055006129 active site 316055006130 tetramer interface [polypeptide binding]; other site 316055006131 Stringent starvation protein B; Region: SspB; pfam04386 316055006132 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 316055006133 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 316055006134 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 316055006135 thymidylate synthase; Reviewed; Region: thyA; PRK01827 316055006136 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 316055006137 dimerization interface [polypeptide binding]; other site 316055006138 active site 316055006139 thymidylate synthase; Reviewed; Region: thyA; PRK01827 316055006140 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 316055006141 dimerization interface [polypeptide binding]; other site 316055006142 active site 316055006143 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 316055006144 active site 316055006145 nucleophile elbow; other site 316055006146 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 316055006147 ATP binding site [chemical binding]; other site 316055006148 putative Mg++ binding site [ion binding]; other site 316055006149 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 316055006150 nucleotide binding region [chemical binding]; other site 316055006151 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 316055006152 ATP-binding site [chemical binding]; other site 316055006153 Nuclease-related domain; Region: NERD; pfam08378 316055006154 Part of AAA domain; Region: AAA_19; pfam13245 316055006155 Family description; Region: UvrD_C_2; pfam13538 316055006156 DEAD/DEAH box helicase; Region: DEAD; pfam00270 316055006157 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 316055006158 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055006159 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 316055006160 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 316055006161 ATP binding site [chemical binding]; other site 316055006162 Mg2+ binding site [ion binding]; other site 316055006163 G-X-G motif; other site 316055006164 Domain of unknown function (DUF4338); Region: DUF4338; pfam14236 316055006165 Domain of unknown function (DUF4338); Region: DUF4338; pfam14236 316055006166 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006167 Walker A motif; other site 316055006168 ATP binding site [chemical binding]; other site 316055006169 Walker B motif; other site 316055006170 Peptidase family M41; Region: Peptidase_M41; pfam01434 316055006171 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 316055006172 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 316055006173 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 316055006174 folate binding site [chemical binding]; other site 316055006175 NADP+ binding site [chemical binding]; other site 316055006176 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 316055006177 HflK protein; Region: hflK; TIGR01933 316055006178 FtsH protease regulator HflC; Provisional; Region: PRK11029 316055006179 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 316055006180 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 316055006181 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 316055006182 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055006183 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055006184 protein binding site [polypeptide binding]; other site 316055006185 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 316055006186 protein binding site [polypeptide binding]; other site 316055006187 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 316055006188 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 316055006189 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 316055006190 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 316055006191 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 316055006192 motif II; other site 316055006193 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 316055006194 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 316055006195 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 316055006196 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055006197 PYR/PP interface [polypeptide binding]; other site 316055006198 dimer interface [polypeptide binding]; other site 316055006199 TPP binding site [chemical binding]; other site 316055006200 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316055006201 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 316055006202 TPP-binding site [chemical binding]; other site 316055006203 dimer interface [polypeptide binding]; other site 316055006204 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 316055006205 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 316055006206 tetramer interface [polypeptide binding]; other site 316055006207 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055006208 catalytic residue [active] 316055006209 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 316055006210 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 316055006211 putative valine binding site [chemical binding]; other site 316055006212 dimer interface [polypeptide binding]; other site 316055006213 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 316055006214 Protein required for attachment to host cells; Region: Host_attach; pfam10116 316055006215 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 316055006216 PemK-like protein; Region: PemK; cl00995 316055006217 ketol-acid reductoisomerase; Provisional; Region: PRK05479 316055006218 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 316055006219 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 316055006220 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 316055006221 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 316055006222 S-adenosylmethionine binding site [chemical binding]; other site 316055006223 short chain dehydrogenase; Validated; Region: PRK06182 316055006224 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 316055006225 NADP binding site [chemical binding]; other site 316055006226 active site 316055006227 steroid binding site; other site 316055006228 Sulfatase; Region: Sulfatase; cl17466 316055006229 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 316055006230 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 316055006231 putative substrate translocation pore; other site 316055006232 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055006233 dimer interface [polypeptide binding]; other site 316055006234 conserved gate region; other site 316055006235 putative PBP binding loops; other site 316055006236 ABC-ATPase subunit interface; other site 316055006237 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 316055006238 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 316055006239 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055006240 Walker A/P-loop; other site 316055006241 ATP binding site [chemical binding]; other site 316055006242 Q-loop/lid; other site 316055006243 ABC transporter signature motif; other site 316055006244 Walker B; other site 316055006245 D-loop; other site 316055006246 H-loop/switch region; other site 316055006247 Protein of unknown function (DUF2283); Region: DUF2283; pfam10049 316055006248 NUDIX domain; Region: NUDIX; pfam00293 316055006249 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 316055006250 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 316055006251 biotin synthase; Region: bioB; TIGR00433 316055006252 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 316055006253 FeS/SAM binding site; other site 316055006254 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 316055006255 2-isopropylmalate synthase; Validated; Region: PRK00915 316055006256 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 316055006257 active site 316055006258 catalytic residues [active] 316055006259 metal binding site [ion binding]; metal-binding site 316055006260 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 316055006261 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 316055006262 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 316055006263 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 316055006264 DctM-like transporters; Region: DctM; pfam06808 316055006265 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 316055006266 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 316055006267 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 316055006268 active site 316055006269 TDP-binding site; other site 316055006270 acceptor substrate-binding pocket; other site 316055006271 homodimer interface [polypeptide binding]; other site 316055006272 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 316055006273 active site 316055006274 SAM binding site [chemical binding]; other site 316055006275 homodimer interface [polypeptide binding]; other site 316055006276 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 316055006277 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055006278 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 316055006279 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 316055006280 active site 316055006281 SAM binding site [chemical binding]; other site 316055006282 homodimer interface [polypeptide binding]; other site 316055006283 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 316055006284 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 316055006285 active site 316055006286 putative homodimer interface [polypeptide binding]; other site 316055006287 SAM binding site [chemical binding]; other site 316055006288 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 316055006289 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055006290 S-adenosylmethionine binding site [chemical binding]; other site 316055006291 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; pfam02571 316055006292 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 316055006293 active site 316055006294 SAM binding site [chemical binding]; other site 316055006295 homodimer interface [polypeptide binding]; other site 316055006296 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 316055006297 active site 316055006298 SAM binding site [chemical binding]; other site 316055006299 homodimer interface [polypeptide binding]; other site 316055006300 precorrin-8X methylmutase; Reviewed; Region: cobH; PRK08285 316055006301 Precorrin-8X methylmutase; Region: CbiC; pfam02570 316055006302 CitB domain protein; Region: CitB; TIGR02484 316055006303 tricarballylate dehydrogenase; Validated; Region: PRK08274 316055006304 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055006305 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 316055006306 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 316055006307 putative dimer interface [polypeptide binding]; other site 316055006308 active site pocket [active] 316055006309 putative cataytic base [active] 316055006310 Precorrin-6A synthase, the cobalamin biosynthesis enzyme CobF; Region: Precorrin-6A-synthase; cd11643 316055006311 active site 316055006312 SAM binding site [chemical binding]; other site 316055006313 homodimer interface [polypeptide binding]; other site 316055006314 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(P)...; Region: BluB; cd02145 316055006315 putative FMN binding site [chemical binding]; other site 316055006316 Protein of unknown function (DUF1636); Region: DUF1636; pfam07845 316055006317 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 316055006318 homotrimer interface [polypeptide binding]; other site 316055006319 Walker A motif; other site 316055006320 GTP binding site [chemical binding]; other site 316055006321 Walker B motif; other site 316055006322 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 316055006323 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 316055006324 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 316055006325 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 316055006326 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 316055006327 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 316055006328 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 316055006329 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 316055006330 homodimer interface [polypeptide binding]; other site 316055006331 Walker A motif; other site 316055006332 ATP binding site [chemical binding]; other site 316055006333 hydroxycobalamin binding site [chemical binding]; other site 316055006334 Walker B motif; other site 316055006335 cobyric acid synthase; Provisional; Region: PRK00784 316055006336 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055006337 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055006338 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 316055006339 catalytic triad [active] 316055006340 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 316055006341 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 316055006342 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 316055006343 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055006344 catalytic residue [active] 316055006345 Predicted periplasmic protein [Function unknown]; Region: COG3904 316055006346 Protein of unknown function (DUF3750); Region: DUF3750; pfam12570 316055006347 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055006348 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055006349 dimer interface [polypeptide binding]; other site 316055006350 phosphorylation site [posttranslational modification] 316055006351 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 316055006352 ATP binding site [chemical binding]; other site 316055006353 Mg2+ binding site [ion binding]; other site 316055006354 G-X-G motif; other site 316055006355 Response regulator receiver domain; Region: Response_reg; pfam00072 316055006356 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 316055006357 active site 316055006358 phosphorylation site [posttranslational modification] 316055006359 intermolecular recognition site; other site 316055006360 dimerization interface [polypeptide binding]; other site 316055006361 Cytochrome c; Region: Cytochrom_C; cl11414 316055006362 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055006363 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055006364 active site 316055006365 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055006366 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055006367 active site 316055006368 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055006369 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 316055006370 putative C-terminal domain interface [polypeptide binding]; other site 316055006371 putative GSH binding site (G-site) [chemical binding]; other site 316055006372 putative dimer interface [polypeptide binding]; other site 316055006373 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 316055006374 N-terminal domain interface [polypeptide binding]; other site 316055006375 dimer interface [polypeptide binding]; other site 316055006376 substrate binding pocket (H-site) [chemical binding]; other site 316055006377 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316055006378 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 316055006379 acyl-CoA synthetase; Validated; Region: PRK08316 316055006380 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055006381 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055006382 acyl-activating enzyme (AAE) consensus motif; other site 316055006383 acyl-activating enzyme (AAE) consensus motif; other site 316055006384 putative AMP binding site [chemical binding]; other site 316055006385 putative active site [active] 316055006386 putative CoA binding site [chemical binding]; other site 316055006387 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 316055006388 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 316055006389 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 316055006390 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 316055006391 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055006392 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 316055006393 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 316055006394 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 316055006395 carboxyltransferase (CT) interaction site; other site 316055006396 biotinylation site [posttranslational modification]; other site 316055006397 enoyl-CoA hydratase; Provisional; Region: PRK05995 316055006398 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 316055006399 substrate binding site [chemical binding]; other site 316055006400 oxyanion hole (OAH) forming residues; other site 316055006401 trimer interface [polypeptide binding]; other site 316055006402 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055006403 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055006404 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 316055006405 EamA-like transporter family; Region: EamA; pfam00892 316055006406 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 316055006407 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 316055006408 NAD binding site [chemical binding]; other site 316055006409 catalytic residues [active] 316055006410 dihydroxy-acid dehydratase; Validated; Region: PRK06131 316055006411 Protein of unknown function (DUF2778); Region: DUF2778; pfam10908 316055006412 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 316055006413 Protein of unknown function DUF262; Region: DUF262; pfam03235 316055006414 Uncharacterized conserved protein [Function unknown]; Region: COG1479 316055006415 Domain of unknown function (DUF2383); Region: DUF2383; pfam09537 316055006416 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055006417 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 316055006418 NAD(P) binding site [chemical binding]; other site 316055006419 active site 316055006420 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 316055006421 dimerization interface [polypeptide binding]; other site 316055006422 putative DNA binding site [nucleotide binding]; other site 316055006423 putative Zn2+ binding site [ion binding]; other site 316055006424 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 316055006425 dimerization interface [polypeptide binding]; other site 316055006426 putative DNA binding site [nucleotide binding]; other site 316055006427 putative Zn2+ binding site [ion binding]; other site 316055006428 Uncharacterized protein containing caspase domain [General function prediction only]; Region: COG4249 316055006429 Caspase domain; Region: Peptidase_C14; pfam00656 316055006430 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055006431 MarR family; Region: MarR; pfam01047 316055006432 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055006433 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055006434 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 316055006435 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055006436 nucleophilic elbow; other site 316055006437 catalytic triad; other site 316055006438 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055006439 GIY-YIG motif/motif A; other site 316055006440 putative active site [active] 316055006441 putative metal binding site [ion binding]; other site 316055006442 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055006443 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 316055006444 S-adenosylmethionine binding site [chemical binding]; other site 316055006445 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 316055006446 GIY-YIG motif/motif A; other site 316055006447 putative active site [active] 316055006448 putative metal binding site [ion binding]; other site 316055006449 yecA family protein; Region: ygfB_yecA; TIGR02292 316055006450 SEC-C motif; Region: SEC-C; pfam02810 316055006451 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 316055006452 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 316055006453 ring oligomerisation interface [polypeptide binding]; other site 316055006454 ATP/Mg binding site [chemical binding]; other site 316055006455 stacking interactions; other site 316055006456 hinge regions; other site 316055006457 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 316055006458 oligomerisation interface [polypeptide binding]; other site 316055006459 mobile loop; other site 316055006460 roof hairpin; other site 316055006461 Usg-like family; Region: Usg; pfam06233 316055006462 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 316055006463 AAA domain; Region: AAA_33; pfam13671 316055006464 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 316055006465 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 316055006466 Nucleoside recognition; Region: Gate; pfam07670 316055006467 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 316055006468 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055006469 dimer interface [polypeptide binding]; other site 316055006470 phosphorylation site [posttranslational modification] 316055006471 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 316055006472 ATP binding site [chemical binding]; other site 316055006473 Mg2+ binding site [ion binding]; other site 316055006474 G-X-G motif; other site 316055006475 Response regulator receiver domain; Region: Response_reg; pfam00072 316055006476 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 316055006477 active site 316055006478 phosphorylation site [posttranslational modification] 316055006479 intermolecular recognition site; other site 316055006480 dimerization interface [polypeptide binding]; other site 316055006481 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 316055006482 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055006483 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 316055006484 classical (c) SDRs; Region: SDR_c; cd05233 316055006485 NAD(P) binding site [chemical binding]; other site 316055006486 active site 316055006487 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055006488 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055006489 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055006490 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 316055006491 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 316055006492 active site 316055006493 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055006494 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 316055006495 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055006496 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 316055006497 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 316055006498 Uncharacterized conserved protein [Function unknown]; Region: COG2308 316055006499 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 316055006500 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 316055006501 putative MPT binding site; other site 316055006502 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055006503 active site 316055006504 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 316055006505 substrate binding site [chemical binding]; other site 316055006506 methionine synthase; Provisional; Region: PRK01207 316055006507 THF binding site; other site 316055006508 zinc-binding site [ion binding]; other site 316055006509 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 316055006510 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 316055006511 C-terminal domain interface [polypeptide binding]; other site 316055006512 GSH binding site (G-site) [chemical binding]; other site 316055006513 dimer interface [polypeptide binding]; other site 316055006514 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 316055006515 N-terminal domain interface [polypeptide binding]; other site 316055006516 putative dimer interface [polypeptide binding]; other site 316055006517 active site 316055006518 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 316055006519 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 316055006520 putative catalytic residue [active] 316055006521 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 316055006522 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 316055006523 NAD(P) binding site [chemical binding]; other site 316055006524 enoyl-CoA hydratase; Provisional; Region: PRK08260 316055006525 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 316055006526 substrate binding site [chemical binding]; other site 316055006527 oxyanion hole (OAH) forming residues; other site 316055006528 trimer interface [polypeptide binding]; other site 316055006529 salicylate hydroxylase; Provisional; Region: PRK08163 316055006530 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055006531 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 316055006532 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055006533 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055006534 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 316055006535 serine acetyltransferase; Provisional; Region: cysE; PRK11132 316055006536 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 316055006537 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 316055006538 trimer interface [polypeptide binding]; other site 316055006539 active site 316055006540 substrate binding site [chemical binding]; other site 316055006541 CoA binding site [chemical binding]; other site 316055006542 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 316055006543 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 316055006544 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 316055006545 trimer interface [polypeptide binding]; other site 316055006546 putative metal binding site [ion binding]; other site 316055006547 Ribbon-helix-helix domain; Region: RHH_3; pfam12651 316055006548 Porin subfamily; Region: Porin_2; pfam02530 316055006549 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055006550 MarR family; Region: MarR_2; pfam12802 316055006551 Autoinducer synthetase; Region: Autoind_synth; cl17404 316055006552 Autoinducer binding domain; Region: Autoind_bind; pfam03472 316055006553 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055006554 DNA binding residues [nucleotide binding] 316055006555 dimerization interface [polypeptide binding]; other site 316055006556 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; pfam06035 316055006557 PilZ domain; Region: PilZ; pfam07238 316055006558 PilZ domain; Region: PilZ; pfam07238 316055006559 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055006560 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 316055006561 ligand binding site [chemical binding]; other site 316055006562 flexible hinge region; other site 316055006563 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055006564 PAS domain; Region: PAS_5; pfam07310 316055006565 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 316055006566 Rhomboid family; Region: Rhomboid; cl11446 316055006567 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 316055006568 FOG: CBS domain [General function prediction only]; Region: COG0517 316055006569 hypothetical protein; Provisional; Region: PRK10279 316055006570 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 316055006571 nucleophile elbow; other site 316055006572 PAS domain S-box; Region: sensory_box; TIGR00229 316055006573 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 316055006574 putative active site [active] 316055006575 heme pocket [chemical binding]; other site 316055006576 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055006577 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055006578 metal binding site [ion binding]; metal-binding site 316055006579 active site 316055006580 I-site; other site 316055006581 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 316055006582 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 316055006583 putative FMN binding site [chemical binding]; other site 316055006584 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 316055006585 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 316055006586 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 316055006587 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 316055006588 active site 316055006589 dimer interface [polypeptide binding]; other site 316055006590 motif 1; other site 316055006591 motif 2; other site 316055006592 motif 3; other site 316055006593 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 316055006594 anticodon binding site; other site 316055006595 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 316055006596 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 316055006597 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 316055006598 putative substrate translocation pore; other site 316055006599 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 316055006600 Methyltransferase domain; Region: Methyltransf_24; pfam13578 316055006601 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055006602 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055006603 Protein of unknown function (DUF3574); Region: DUF3574; pfam12098 316055006604 hypothetical protein; Validated; Region: PRK00041 316055006605 Predicted periplasmic protein [Function unknown]; Region: COG3904 316055006606 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 316055006607 Probable galactinol--sucrose galactosyltransferase; Region: PLN02711 316055006608 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 316055006609 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 316055006610 trimerization site [polypeptide binding]; other site 316055006611 active site 316055006612 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 316055006613 GTP cyclohydrolase I; Provisional; Region: PLN03044 316055006614 active site 316055006615 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 316055006616 Cytochrome b5-like Heme/Steroid binding domain; Region: Cyt-b5; pfam00173 316055006617 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 316055006618 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 316055006619 FAD binding pocket [chemical binding]; other site 316055006620 conserved FAD binding motif [chemical binding]; other site 316055006621 phosphate binding motif [ion binding]; other site 316055006622 beta-alpha-beta structure motif; other site 316055006623 NAD binding pocket [chemical binding]; other site 316055006624 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055006625 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055006626 catalytic residue [active] 316055006627 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055006628 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 316055006629 putative binding surface; other site 316055006630 active site 316055006631 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055006632 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 316055006633 active site 316055006634 phosphorylation site [posttranslational modification] 316055006635 intermolecular recognition site; other site 316055006636 dimerization interface [polypeptide binding]; other site 316055006637 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055006638 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055006639 metal binding site [ion binding]; metal-binding site 316055006640 active site 316055006641 I-site; other site 316055006642 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 316055006643 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 316055006644 TPR motif; other site 316055006645 TPR repeat; Region: TPR_11; pfam13414 316055006646 binding surface 316055006647 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055006648 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055006649 DNA-binding site [nucleotide binding]; DNA binding site 316055006650 RNA-binding motif; other site 316055006651 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 316055006652 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055006653 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 316055006654 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 316055006655 active site 316055006656 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 316055006657 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055006658 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055006659 acyl-activating enzyme (AAE) consensus motif; other site 316055006660 acyl-activating enzyme (AAE) consensus motif; other site 316055006661 putative AMP binding site [chemical binding]; other site 316055006662 putative active site [active] 316055006663 putative CoA binding site [chemical binding]; other site 316055006664 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 316055006665 active site 1 [active] 316055006666 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 316055006667 CoA binding domain; Region: CoA_binding_2; pfam13380 316055006668 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 316055006669 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 316055006670 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 316055006671 short chain dehydrogenase; Provisional; Region: PRK06197 316055006672 putative NAD(P) binding site [chemical binding]; other site 316055006673 active site 316055006674 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 316055006675 carboxyltransferase (CT) interaction site; other site 316055006676 biotinylation site [posttranslational modification]; other site 316055006677 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 316055006678 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 316055006679 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 316055006680 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055006681 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055006682 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 316055006683 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 316055006684 tetrameric interface [polypeptide binding]; other site 316055006685 NAD binding site [chemical binding]; other site 316055006686 catalytic residues [active] 316055006687 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 316055006688 homotetrameric interface [polypeptide binding]; other site 316055006689 putative active site [active] 316055006690 metal binding site [ion binding]; metal-binding site 316055006691 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055006692 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 316055006693 substrate binding pocket [chemical binding]; other site 316055006694 FAD binding site [chemical binding]; other site 316055006695 catalytic base [active] 316055006696 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 316055006697 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 316055006698 substrate binding site [chemical binding]; other site 316055006699 oxyanion hole (OAH) forming residues; other site 316055006700 trimer interface [polypeptide binding]; other site 316055006701 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 316055006702 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 316055006703 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 316055006704 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 316055006705 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_1; cd05974 316055006706 active site 316055006707 acyl-activating enzyme (AAE) consensus motif; other site 316055006708 putative CoA binding site [chemical binding]; other site 316055006709 AMP binding site [chemical binding]; other site 316055006710 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 316055006711 putative active site [active] 316055006712 putative catalytic site [active] 316055006713 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055006714 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 316055006715 NAD(P) binding site [chemical binding]; other site 316055006716 active site 316055006717 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 316055006718 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055006719 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 316055006720 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 316055006721 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055006722 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055006723 hypothetical protein; Validated; Region: PRK00124 316055006724 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 316055006725 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 316055006726 catalytic triad [active] 316055006727 putative active site [active] 316055006728 Autotransporter beta-domain; Region: Autotransporter; smart00869 316055006729 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl17426 316055006730 folate binding site [chemical binding]; other site 316055006731 NADP+ binding site [chemical binding]; other site 316055006732 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 316055006733 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 316055006734 NodB motif; other site 316055006735 active site 316055006736 catalytic site [active] 316055006737 metal binding site [ion binding]; metal-binding site 316055006738 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 316055006739 catalytic residues [active] 316055006740 dimer interface [polypeptide binding]; other site 316055006741 hypothetical protein; Provisional; Region: PRK06132 316055006742 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055006743 CreA protein; Region: CreA; pfam05981 316055006744 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 316055006745 Histidine kinase; Region: HisKA_2; pfam07568 316055006746 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055006747 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 316055006748 ATP binding site [chemical binding]; other site 316055006749 Mg2+ binding site [ion binding]; other site 316055006750 G-X-G motif; other site 316055006751 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 316055006752 CoenzymeA binding site [chemical binding]; other site 316055006753 subunit interaction site [polypeptide binding]; other site 316055006754 PHB binding site; other site 316055006755 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055006756 Coenzyme A binding pocket [chemical binding]; other site 316055006757 MgtC family; Region: MgtC; pfam02308 316055006758 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316055006759 Sel1-like repeats; Region: SEL1; smart00671 316055006760 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; pfam09939 316055006761 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 316055006762 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 316055006763 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 316055006764 CAAX protease self-immunity; Region: Abi; pfam02517 316055006765 CHASE3 domain; Region: CHASE3; pfam05227 316055006766 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 316055006767 dimer interface [polypeptide binding]; other site 316055006768 phosphorylation site [posttranslational modification] 316055006769 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 316055006770 ATP binding site [chemical binding]; other site 316055006771 Mg2+ binding site [ion binding]; other site 316055006772 G-X-G motif; other site 316055006773 Predicted flavoprotein [General function prediction only]; Region: COG0431 316055006774 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 316055006775 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 316055006776 Domain of unknown function (DUF4062); Region: DUF4062; pfam13271 316055006777 TniQ; Region: TniQ; pfam06527 316055006778 AAA domain; Region: AAA_22; pfam13401 316055006779 Integrase core domain; Region: rve; pfam00665 316055006780 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316055006781 Transposase; Region: HTH_Tnp_1; pfam01527 316055006782 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 316055006783 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055006784 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 316055006785 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055006786 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 316055006787 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055006788 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055006789 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006790 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 316055006791 Walker A motif; other site 316055006792 ATP binding site [chemical binding]; other site 316055006793 Walker B motif; other site 316055006794 arginine finger; other site 316055006795 Peptidase family M41; Region: Peptidase_M41; pfam01434 316055006796 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 316055006797 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 316055006798 non-specific DNA binding site [nucleotide binding]; other site 316055006799 salt bridge; other site 316055006800 sequence-specific DNA binding site [nucleotide binding]; other site 316055006801 Restriction endonuclease; Region: Mrr_cat; pfam04471 316055006802 chromosome segregation protein; Provisional; Region: PRK02224 316055006803 Domain of unknown function (DUF4016); Region: DUF4016; pfam13208 316055006804 tellurite resistance protein terB; Region: terB; cd07176 316055006805 putative metal binding site [ion binding]; other site 316055006806 P-loop Domain of unknown function (DUF2791); Region: DUF2791; pfam10923 316055006807 AAA ATPase domain; Region: AAA_16; pfam13191 316055006808 DEAD-like helicases superfamily; Region: DEXDc; smart00487 316055006809 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 316055006810 ATP binding site [chemical binding]; other site 316055006811 putative Mg++ binding site [ion binding]; other site 316055006812 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 316055006813 nucleotide binding region [chemical binding]; other site 316055006814 ATP-binding site [chemical binding]; other site 316055006815 PBP superfamily domain; Region: PBP_like_2; pfam12849 316055006816 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 316055006817 PAS domain S-box; Region: sensory_box; TIGR00229 316055006818 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055006819 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055006820 metal binding site [ion binding]; metal-binding site 316055006821 active site 316055006822 I-site; other site 316055006823 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 316055006824 Sensors of blue-light using FAD; Region: BLUF; smart01034 316055006825 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 316055006826 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055006827 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055006828 dimerization interface [polypeptide binding]; other site 316055006829 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055006830 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055006831 dimer interface [polypeptide binding]; other site 316055006832 putative CheW interface [polypeptide binding]; other site 316055006833 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055006834 dimerization interface [polypeptide binding]; other site 316055006835 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055006836 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055006837 dimer interface [polypeptide binding]; other site 316055006838 putative CheW interface [polypeptide binding]; other site 316055006839 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055006840 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055006841 metal binding site [ion binding]; metal-binding site 316055006842 active site 316055006843 I-site; other site 316055006844 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 316055006845 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316055006846 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 316055006847 active site 316055006848 metal binding site [ion binding]; metal-binding site 316055006849 Putative serine esterase (DUF676); Region: DUF676; pfam05057 316055006850 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055006851 AAA domain; Region: AAA_22; pfam13401 316055006852 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 316055006853 active site 316055006854 NTP binding site [chemical binding]; other site 316055006855 metal binding triad [ion binding]; metal-binding site 316055006856 HORMA domain; Region: HORMA; pfam02301 316055006857 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 316055006858 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006859 Walker A motif; other site 316055006860 ATP binding site [chemical binding]; other site 316055006861 Walker B motif; other site 316055006862 arginine finger; other site 316055006863 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; pfam09954 316055006864 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 316055006865 non-specific DNA binding site [nucleotide binding]; other site 316055006866 salt bridge; other site 316055006867 sequence-specific DNA binding site [nucleotide binding]; other site 316055006868 Domain of unknown function (DUF955); Region: DUF955; pfam06114 316055006869 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 316055006870 active site 316055006871 catalytic site [active] 316055006872 substrate binding site [chemical binding]; other site 316055006873 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 316055006874 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 316055006875 AAA domain; Region: AAA_30; pfam13604 316055006876 Family description; Region: UvrD_C_2; pfam13538 316055006877 Intermediate filament protein; Region: Filament; pfam00038 316055006878 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 316055006879 active site 316055006880 catalytic residues [active] 316055006881 DNA binding site [nucleotide binding] 316055006882 Int/Topo IB signature motif; other site 316055006883 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 316055006884 active site 316055006885 catalytic residues [active] 316055006886 DNA binding site [nucleotide binding] 316055006887 Int/Topo IB signature motif; other site 316055006888 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055006889 Walker A/P-loop; other site 316055006890 ATP binding site [chemical binding]; other site 316055006891 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055006892 ABC transporter signature motif; other site 316055006893 Walker B; other site 316055006894 D-loop; other site 316055006895 H-loop/switch region; other site 316055006896 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 316055006897 ATP binding site [chemical binding]; other site 316055006898 Mg2+ binding site [ion binding]; other site 316055006899 G-X-G motif; other site 316055006900 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006901 AAA domain; Region: AAA_22; pfam13401 316055006902 Walker A motif; other site 316055006903 ATP binding site [chemical binding]; other site 316055006904 Walker B motif; other site 316055006905 Peptidase family M41; Region: Peptidase_M41; pfam01434 316055006906 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 316055006907 non-specific DNA binding site [nucleotide binding]; other site 316055006908 salt bridge; other site 316055006909 sequence-specific DNA binding site [nucleotide binding]; other site 316055006910 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 316055006911 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 316055006912 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 316055006913 active site 316055006914 nucleophile elbow; other site 316055006915 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 316055006916 active site 316055006917 NTP binding site [chemical binding]; other site 316055006918 metal binding triad [ion binding]; metal-binding site 316055006919 Domain of unknown function (DUF955); Region: DUF955; pfam06114 316055006920 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 316055006921 Helix-turn-helix domain; Region: HTH_17; cl17695 316055006922 Caspase domain; Region: Peptidase_C14; pfam00656 316055006923 ski2-like helicase; Provisional; Region: PRK00254 316055006924 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 316055006925 ATP binding site [chemical binding]; other site 316055006926 putative Mg++ binding site [ion binding]; other site 316055006927 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 316055006928 nucleotide binding region [chemical binding]; other site 316055006929 ATP-binding site [chemical binding]; other site 316055006930 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 316055006931 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 316055006932 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 316055006933 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 316055006934 active site 316055006935 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 316055006936 TSCPD domain; Region: TSCPD; pfam12637 316055006937 EamA-like transporter family; Region: EamA; pfam00892 316055006938 glutamine synthetase; Provisional; Region: glnA; PRK09469 316055006939 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 316055006940 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 316055006941 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 316055006942 Nitrogen regulatory protein P-II; Region: P-II; smart00938 316055006943 Uncharacterized conserved protein [Function unknown]; Region: COG0062 316055006944 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 316055006945 putative substrate binding site [chemical binding]; other site 316055006946 putative ATP binding site [chemical binding]; other site 316055006947 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 316055006948 Multicopper oxidase; Region: Cu-oxidase; pfam00394 316055006949 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 316055006950 trigger factor; Provisional; Region: tig; PRK01490 316055006951 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 316055006952 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 316055006953 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 316055006954 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 316055006955 oligomer interface [polypeptide binding]; other site 316055006956 active site residues [active] 316055006957 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 316055006958 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 316055006959 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006960 Walker A motif; other site 316055006961 ATP binding site [chemical binding]; other site 316055006962 Walker B motif; other site 316055006963 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 316055006964 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 316055006965 Found in ATP-dependent protease La (LON); Region: LON; smart00464 316055006966 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055006967 Walker A motif; other site 316055006968 ATP binding site [chemical binding]; other site 316055006969 Walker B motif; other site 316055006970 arginine finger; other site 316055006971 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 316055006972 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 316055006973 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055006974 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055006975 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055006976 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 316055006977 peptidase T; Region: peptidase-T; TIGR01882 316055006978 metal binding site [ion binding]; metal-binding site 316055006979 dimer interface [polypeptide binding]; other site 316055006980 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 316055006981 IHF dimer interface [polypeptide binding]; other site 316055006982 IHF - DNA interface [nucleotide binding]; other site 316055006983 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 316055006984 binding surface 316055006985 TPR motif; other site 316055006986 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 316055006987 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 316055006988 binding surface 316055006989 TPR motif; other site 316055006990 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 316055006991 binding surface 316055006992 TPR motif; other site 316055006993 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 316055006994 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 316055006995 NADH dehydrogenase subunit B; Validated; Region: PRK06411 316055006996 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 316055006997 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 316055006998 hypothetical protein; Reviewed; Region: PRK12275 316055006999 four helix bundle protein; Region: TIGR02436 316055007000 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 316055007001 NADH dehydrogenase subunit D; Validated; Region: PRK06075 316055007002 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055007003 NADH dehydrogenase subunit E; Validated; Region: PRK07539 316055007004 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 316055007005 putative dimer interface [polypeptide binding]; other site 316055007006 [2Fe-2S] cluster binding site [ion binding]; other site 316055007007 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 316055007008 SLBB domain; Region: SLBB; pfam10531 316055007009 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 316055007010 NADH dehydrogenase subunit G; Validated; Region: PRK09130 316055007011 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 316055007012 catalytic loop [active] 316055007013 iron binding site [ion binding]; other site 316055007014 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 316055007015 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 316055007016 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 316055007017 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 316055007018 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 316055007019 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 316055007020 4Fe-4S binding domain; Region: Fer4; pfam00037 316055007021 4Fe-4S binding domain; Region: Fer4; pfam00037 316055007022 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 316055007023 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 316055007024 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 316055007025 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 316055007026 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 316055007027 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 316055007028 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055007029 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 316055007030 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055007031 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 316055007032 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055007033 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 316055007034 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 316055007035 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 316055007036 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 316055007037 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055007038 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 316055007039 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055007040 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 316055007041 dimer interface [polypeptide binding]; other site 316055007042 substrate binding site [chemical binding]; other site 316055007043 metal binding site [ion binding]; metal-binding site 316055007044 Protein of unknown function (DUF1467); Region: DUF1467; pfam07330 316055007045 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 316055007046 Protein of unknown function (DUF461); Region: DUF461; pfam04314 316055007047 prolyl-tRNA synthetase; Provisional; Region: PRK12325 316055007048 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 316055007049 dimer interface [polypeptide binding]; other site 316055007050 motif 1; other site 316055007051 active site 316055007052 motif 2; other site 316055007053 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 316055007054 active site 316055007055 motif 3; other site 316055007056 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 316055007057 anticodon binding site; other site 316055007058 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 316055007059 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 316055007060 FtsX-like permease family; Region: FtsX; pfam02687 316055007061 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055007062 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055007063 Walker A/P-loop; other site 316055007064 ATP binding site [chemical binding]; other site 316055007065 Q-loop/lid; other site 316055007066 ABC transporter signature motif; other site 316055007067 Walker B; other site 316055007068 D-loop; other site 316055007069 H-loop/switch region; other site 316055007070 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055007071 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055007072 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055007073 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 316055007074 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 316055007075 putative active site [active] 316055007076 putative PHP Thumb interface [polypeptide binding]; other site 316055007077 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 316055007078 generic binding surface I; other site 316055007079 generic binding surface II; other site 316055007080 Uncharacterized protein conserved in bacteria (DUF2191); Region: DUF2191; pfam09957 316055007081 PIN domain of the Rv0301 toxin of Mycobacterium tuberculosis and other uncharacterized, annotated PilT protein domain proteins; Region: PIN_MtRv0301; cd09882 316055007082 putative active site [active] 316055007083 30S ribosomal protein S2/unknown domain fusion protein; Provisional; Region: rpsB; PRK12311 316055007084 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 316055007085 rRNA interaction site [nucleotide binding]; other site 316055007086 S8 interaction site; other site 316055007087 putative laminin-1 binding site; other site 316055007088 Uncharacterized conserved protein [Function unknown]; Region: COG3743 316055007089 elongation factor Ts; Provisional; Region: tsf; PRK09377 316055007090 UBA/TS-N domain; Region: UBA; pfam00627 316055007091 Elongation factor TS; Region: EF_TS; pfam00889 316055007092 Elongation factor TS; Region: EF_TS; pfam00889 316055007093 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 316055007094 putative nucleotide binding site [chemical binding]; other site 316055007095 uridine monophosphate binding site [chemical binding]; other site 316055007096 homohexameric interface [polypeptide binding]; other site 316055007097 ribosome recycling factor; Reviewed; Region: frr; PRK00083 316055007098 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 316055007099 hinge region; other site 316055007100 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14834 316055007101 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 316055007102 catalytic residue [active] 316055007103 putative FPP diphosphate binding site; other site 316055007104 putative FPP binding hydrophobic cleft; other site 316055007105 dimer interface [polypeptide binding]; other site 316055007106 putative IPP diphosphate binding site; other site 316055007107 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 316055007108 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 316055007109 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 316055007110 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 316055007111 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 316055007112 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 316055007113 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 316055007114 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 316055007115 active site 316055007116 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 316055007117 protein binding site [polypeptide binding]; other site 316055007118 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 316055007119 putative substrate binding region [chemical binding]; other site 316055007120 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 316055007121 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 316055007122 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 316055007123 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 316055007124 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 316055007125 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 316055007126 Surface antigen; Region: Bac_surface_Ag; pfam01103 316055007127 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 316055007128 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 316055007129 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 316055007130 trimer interface [polypeptide binding]; other site 316055007131 active site 316055007132 UDP-GlcNAc binding site [chemical binding]; other site 316055007133 lipid binding site [chemical binding]; lipid-binding site 316055007134 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 316055007135 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 316055007136 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 316055007137 active site 316055007138 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 316055007139 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 316055007140 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 316055007141 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 316055007142 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 316055007143 dimer interface [polypeptide binding]; other site 316055007144 active site 316055007145 citrylCoA binding site [chemical binding]; other site 316055007146 NADH binding [chemical binding]; other site 316055007147 cationic pore residues; other site 316055007148 oxalacetate/citrate binding site [chemical binding]; other site 316055007149 coenzyme A binding site [chemical binding]; other site 316055007150 catalytic triad [active] 316055007151 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 316055007152 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 316055007153 HIGH motif; other site 316055007154 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 316055007155 active site 316055007156 KMSKS motif; other site 316055007157 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 316055007158 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316055007159 active site 316055007160 HIGH motif; other site 316055007161 nucleotide binding site [chemical binding]; other site 316055007162 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 316055007163 KMSKS motif; other site 316055007164 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 316055007165 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 316055007166 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 316055007167 Competence protein; Region: Competence; pfam03772 316055007168 LexA repressor; Validated; Region: PRK00215 316055007169 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 316055007170 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 316055007171 Catalytic site [active] 316055007172 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 316055007173 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 316055007174 dimer interface [polypeptide binding]; other site 316055007175 putative functional site; other site 316055007176 putative MPT binding site; other site 316055007177 short chain dehydrogenase; Provisional; Region: PRK05854 316055007178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055007179 NAD(P) binding site [chemical binding]; other site 316055007180 active site 316055007181 BA14K-like protein; Region: BA14K; pfam07886 316055007182 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 316055007183 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 316055007184 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 316055007185 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 316055007186 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055007187 ligand binding site [chemical binding]; other site 316055007188 PilZ domain; Region: PilZ; cl01260 316055007189 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 316055007190 ATPase, P-type (transporting), HAD superfamily, subfamily IC; Region: ATPase_P-type; TIGR01494 316055007191 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316055007192 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 316055007193 motif II; other site 316055007194 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 316055007195 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 316055007196 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 316055007197 putative dimer interface [polypeptide binding]; other site 316055007198 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 316055007199 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 316055007200 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 316055007201 trimer interface [polypeptide binding]; other site 316055007202 active site 316055007203 UDP-GlcNAc binding site [chemical binding]; other site 316055007204 lipid binding site [chemical binding]; lipid-binding site 316055007205 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 316055007206 trimer interface [polypeptide binding]; other site 316055007207 dimer interface [polypeptide binding]; other site 316055007208 putative active site [active] 316055007209 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 316055007210 active site 316055007211 ribulose/triose binding site [chemical binding]; other site 316055007212 phosphate binding site [ion binding]; other site 316055007213 substrate (anthranilate) binding pocket [chemical binding]; other site 316055007214 product (indole) binding pocket [chemical binding]; other site 316055007215 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 316055007216 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 316055007217 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 316055007218 SurA N-terminal domain; Region: SurA_N_3; cl07813 316055007219 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 316055007220 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 316055007221 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 316055007222 triosephosphate isomerase; Provisional; Region: PRK14565 316055007223 substrate binding site [chemical binding]; other site 316055007224 dimer interface [polypeptide binding]; other site 316055007225 catalytic triad [active] 316055007226 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 316055007227 CTP synthetase; Validated; Region: pyrG; PRK05380 316055007228 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 316055007229 Catalytic site [active] 316055007230 active site 316055007231 UTP binding site [chemical binding]; other site 316055007232 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 316055007233 active site 316055007234 putative oxyanion hole; other site 316055007235 catalytic triad [active] 316055007236 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055007237 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055007238 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055007239 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055007240 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 316055007241 PAAR motif; Region: PAAR_motif; pfam05488 316055007242 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 316055007243 Protein of unknown function (DUF497); Region: DUF497; cl01108 316055007244 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 316055007245 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 316055007246 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 316055007247 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional; Region: PRK12775 316055007248 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 316055007249 FAD binding pocket [chemical binding]; other site 316055007250 FAD binding motif [chemical binding]; other site 316055007251 phosphate binding motif [ion binding]; other site 316055007252 beta-alpha-beta structure motif; other site 316055007253 NAD binding pocket [chemical binding]; other site 316055007254 Iron coordination center [ion binding]; other site 316055007255 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055007256 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 316055007257 diiron binding motif [ion binding]; other site 316055007258 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 316055007259 DNA binding residues [nucleotide binding] 316055007260 GAF domain; Region: GAF; pfam01590 316055007261 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 316055007262 choline dehydrogenase; Validated; Region: PRK02106 316055007263 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 316055007264 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 316055007265 enolase; Provisional; Region: eno; PRK00077 316055007266 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 316055007267 dimer interface [polypeptide binding]; other site 316055007268 metal binding site [ion binding]; metal-binding site 316055007269 substrate binding pocket [chemical binding]; other site 316055007270 2-enoyl thioester reductase (ETR) like proteins, child 1; Region: ETR_like_1; cd08291 316055007271 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 316055007272 NADP binding site [chemical binding]; other site 316055007273 dimer interface [polypeptide binding]; other site 316055007274 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 316055007275 Predicted flavoprotein [General function prediction only]; Region: COG0431 316055007276 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 316055007277 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 316055007278 Septum formation initiator; Region: DivIC; pfam04977 316055007279 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 316055007280 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 316055007281 tetramer interface [polypeptide binding]; other site 316055007282 TPP-binding site [chemical binding]; other site 316055007283 heterodimer interface [polypeptide binding]; other site 316055007284 phosphorylation loop region [posttranslational modification] 316055007285 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 316055007286 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 316055007287 E3 interaction surface; other site 316055007288 lipoyl attachment site [posttranslational modification]; other site 316055007289 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 316055007290 alpha subunit interface [polypeptide binding]; other site 316055007291 TPP binding site [chemical binding]; other site 316055007292 heterodimer interface [polypeptide binding]; other site 316055007293 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055007294 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 316055007295 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 316055007296 E3 interaction surface; other site 316055007297 lipoyl attachment site [posttranslational modification]; other site 316055007298 e3 binding domain; Region: E3_binding; pfam02817 316055007299 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 316055007300 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 316055007301 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 316055007302 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 316055007303 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055007304 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 316055007305 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 316055007306 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316055007307 Sel1-like repeats; Region: SEL1; smart00671 316055007308 Sel1-like repeats; Region: SEL1; smart00671 316055007309 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 316055007310 putative catalytic site [active] 316055007311 putative phosphate binding site [ion binding]; other site 316055007312 active site 316055007313 metal binding site A [ion binding]; metal-binding site 316055007314 DNA binding site [nucleotide binding] 316055007315 putative AP binding site [nucleotide binding]; other site 316055007316 putative metal binding site B [ion binding]; other site 316055007317 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055007318 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055007319 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055007320 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 316055007321 Neurotransmitter-gated ion-channel ligand binding domain; Region: Neur_chan_LBD; pfam02931 316055007322 Protein of unknown function (DUF433); Region: DUF433; pfam04255 316055007323 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 316055007324 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 316055007325 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 316055007326 Porin subfamily; Region: Porin_2; pfam02530 316055007327 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 316055007328 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055007329 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055007330 catalytic residue [active] 316055007331 BA14K-like protein; Region: BA14K; pfam07886 316055007332 NADH dehydrogenase; Validated; Region: PRK08183 316055007333 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055007334 TolA protein; Region: tolA_full; TIGR02794 316055007335 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316055007336 RNA polymerase sigma factor; Reviewed; Region: PRK12527 316055007337 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055007338 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 316055007339 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055007340 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 316055007341 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055007342 Walker A motif; other site 316055007343 ATP binding site [chemical binding]; other site 316055007344 Walker B motif; other site 316055007345 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 316055007346 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055007347 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 316055007348 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055007349 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055007350 FecR protein; Region: FecR; pfam04773 316055007351 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 316055007352 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055007353 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055007354 TonB C terminal; Region: TonB_2; pfam13103 316055007355 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 316055007356 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055007357 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055007358 DNA binding residues [nucleotide binding] 316055007359 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055007360 FecR protein; Region: FecR; pfam04773 316055007361 haemagglutination activity domain; Region: Haemagg_act; pfam05860 316055007362 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055007363 Integrase core domain; Region: rve_3; pfam13683 316055007364 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055007365 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 316055007366 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 316055007367 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055007368 DNA binding residues [nucleotide binding] 316055007369 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055007370 FecR protein; Region: FecR; pfam04773 316055007371 haemagglutination activity domain; Region: Haemagg_act; pfam05860 316055007372 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055007373 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 316055007374 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 316055007375 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 316055007376 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 316055007377 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 316055007378 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 316055007379 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 316055007380 type II secretion system protein E; Region: type_II_gspE; TIGR02533 316055007381 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055007382 Walker A motif; other site 316055007383 ATP binding site [chemical binding]; other site 316055007384 Walker B motif; other site 316055007385 Type II secretion system (T2SS), protein M subtype b; Region: T2SM_b; pfam10741 316055007386 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 316055007387 type II secretion system protein D; Region: type_II_gspD; TIGR02517 316055007388 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 316055007389 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 316055007390 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055007391 TPR repeat; Region: TPR_11; pfam13414 316055007392 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 316055007393 TPR motif; other site 316055007394 binding surface 316055007395 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 316055007396 TPR motif; other site 316055007397 binding surface 316055007398 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 316055007399 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 316055007400 TPR repeat; Region: TPR_11; pfam13414 316055007401 binding surface 316055007402 TPR motif; other site 316055007403 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 316055007404 binding surface 316055007405 TPR motif; other site 316055007406 TPR repeat; Region: TPR_11; pfam13414 316055007407 TPR repeat; Region: TPR_11; pfam13414 316055007408 TPR repeat; Region: TPR_11; pfam13414 316055007409 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 316055007410 binding surface 316055007411 TPR motif; other site 316055007412 Tetratricopeptide repeat; Region: TPR_12; pfam13424 316055007413 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 316055007414 binding surface 316055007415 TPR motif; other site 316055007416 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 316055007417 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 316055007418 binding surface 316055007419 TPR motif; other site 316055007420 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 316055007421 PBP superfamily domain; Region: PBP_like_2; cl17296 316055007422 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055007423 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 316055007424 NAD binding site [chemical binding]; other site 316055007425 putative substrate binding site 2 [chemical binding]; other site 316055007426 putative substrate binding site 1 [chemical binding]; other site 316055007427 active site 316055007428 Arginase family; Region: Arginase; cd09989 316055007429 agmatinase; Region: agmatinase; TIGR01230 316055007430 active site 316055007431 Mn binding site [ion binding]; other site 316055007432 oligomer interface [polypeptide binding]; other site 316055007433 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 316055007434 metal binding site [ion binding]; metal-binding site 316055007435 active site 316055007436 phosphoribulokinase; Provisional; Region: PRK15453 316055007437 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 316055007438 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 316055007439 TPP-binding site [chemical binding]; other site 316055007440 dimer interface [polypeptide binding]; other site 316055007441 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 316055007442 PYR/PP interface [polypeptide binding]; other site 316055007443 dimer interface [polypeptide binding]; other site 316055007444 TPP binding site [chemical binding]; other site 316055007445 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055007446 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 316055007447 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 316055007448 intersubunit interface [polypeptide binding]; other site 316055007449 active site 316055007450 zinc binding site [ion binding]; other site 316055007451 Na+ binding site [ion binding]; other site 316055007452 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 316055007453 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 316055007454 dimer interface [polypeptide binding]; other site 316055007455 active site 316055007456 catalytic residue [active] 316055007457 metal binding site [ion binding]; metal-binding site 316055007458 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316055007459 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 316055007460 VanZ like family; Region: VanZ; cl01971 316055007461 Protein of unknown function (DUF3222); Region: DUF3222; pfam11519 316055007462 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 316055007463 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 316055007464 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 316055007465 active site 316055007466 HIGH motif; other site 316055007467 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316055007468 KMSK motif region; other site 316055007469 tRNA binding surface [nucleotide binding]; other site 316055007470 DALR anticodon binding domain; Region: DALR_1; smart00836 316055007471 anticodon binding site; other site 316055007472 Sporulation related domain; Region: SPOR; pfam05036 316055007473 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 316055007474 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 316055007475 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 316055007476 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 316055007477 twin arginine translocase protein A; Provisional; Region: tatA; PRK00720 316055007478 twin arginine-targeting protein translocase TatB; Region: tatB; TIGR01410 316055007479 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 316055007480 seryl-tRNA synthetase; Provisional; Region: PRK05431 316055007481 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 316055007482 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 316055007483 dimer interface [polypeptide binding]; other site 316055007484 active site 316055007485 motif 1; other site 316055007486 motif 2; other site 316055007487 motif 3; other site 316055007488 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 316055007489 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055007490 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 316055007491 active site 316055007492 phosphorylation site [posttranslational modification] 316055007493 intermolecular recognition site; other site 316055007494 dimerization interface [polypeptide binding]; other site 316055007495 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 316055007496 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 316055007497 S-adenosylmethionine binding site [chemical binding]; other site 316055007498 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 316055007499 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 316055007500 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 316055007501 Peptidase family M23; Region: Peptidase_M23; pfam01551 316055007502 Uncharacterized conserved protein [Function unknown]; Region: COG3339 316055007503 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 316055007504 aromatic arch; other site 316055007505 DCoH dimer interaction site [polypeptide binding]; other site 316055007506 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 316055007507 DCoH tetramer interaction site [polypeptide binding]; other site 316055007508 substrate binding site [chemical binding]; other site 316055007509 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 316055007510 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 316055007511 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 316055007512 G1 box; other site 316055007513 putative GEF interaction site [polypeptide binding]; other site 316055007514 GTP/Mg2+ binding site [chemical binding]; other site 316055007515 Switch I region; other site 316055007516 G2 box; other site 316055007517 G3 box; other site 316055007518 Switch II region; other site 316055007519 G4 box; other site 316055007520 G5 box; other site 316055007521 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 316055007522 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 316055007523 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 316055007524 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 316055007525 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055007526 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055007527 Integrase core domain; Region: rve_3; cl15866 316055007528 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055007529 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 316055007530 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055007531 DNA binding residues [nucleotide binding] 316055007532 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055007533 FecR protein; Region: FecR; pfam04773 316055007534 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 316055007535 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055007536 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 316055007537 MG2 domain; Region: A2M_N; pfam01835 316055007538 Alpha-2-macroglobulin family; Region: A2M; pfam00207 316055007539 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 316055007540 surface patch; other site 316055007541 thioester region; other site 316055007542 specificity defining residues; other site 316055007543 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 316055007544 Transglycosylase; Region: Transgly; pfam00912 316055007545 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 316055007546 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 316055007547 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 316055007548 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 316055007549 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 316055007550 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 316055007551 active site 316055007552 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 316055007553 Ligand binding site; other site 316055007554 Putative Catalytic site; other site 316055007555 DXD motif; other site 316055007556 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 316055007557 cystathionine beta-lyase; Provisional; Region: PRK05967 316055007558 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 316055007559 homodimer interface [polypeptide binding]; other site 316055007560 substrate-cofactor binding pocket; other site 316055007561 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055007562 catalytic residue [active] 316055007563 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 316055007564 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055007565 substrate binding pocket [chemical binding]; other site 316055007566 membrane-bound complex binding site; other site 316055007567 hinge residues; other site 316055007568 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 316055007569 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055007570 conserved gate region; other site 316055007571 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055007572 dimer interface [polypeptide binding]; other site 316055007573 ABC-ATPase subunit interface; other site 316055007574 putative PBP binding loops; other site 316055007575 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055007576 dimer interface [polypeptide binding]; other site 316055007577 conserved gate region; other site 316055007578 putative PBP binding loops; other site 316055007579 ABC-ATPase subunit interface; other site 316055007580 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 316055007581 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 316055007582 Walker A/P-loop; other site 316055007583 ATP binding site [chemical binding]; other site 316055007584 Q-loop/lid; other site 316055007585 ABC transporter signature motif; other site 316055007586 Walker B; other site 316055007587 D-loop; other site 316055007588 H-loop/switch region; other site 316055007589 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 316055007590 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 316055007591 dimer interface [polypeptide binding]; other site 316055007592 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055007593 catalytic residue [active] 316055007594 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 316055007595 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 316055007596 S-adenosylmethionine binding site [chemical binding]; other site 316055007597 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 316055007598 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 316055007599 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055007600 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 316055007601 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055007602 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055007603 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055007604 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 316055007605 Protein export membrane protein; Region: SecD_SecF; cl14618 316055007606 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 316055007607 DTW domain; Region: DTW; cl01221 316055007608 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 316055007609 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 316055007610 S-adenosylmethionine binding site [chemical binding]; other site 316055007611 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 316055007612 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 316055007613 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 316055007614 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 316055007615 HIGH motif; other site 316055007616 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 316055007617 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 316055007618 active site 316055007619 KMSKS motif; other site 316055007620 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 316055007621 tRNA binding surface [nucleotide binding]; other site 316055007622 anticodon binding site; other site 316055007623 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 316055007624 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 316055007625 active site 316055007626 DNA binding site [nucleotide binding] 316055007627 lipoyl synthase; Provisional; Region: PRK05481 316055007628 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 316055007629 FeS/SAM binding site; other site 316055007630 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 316055007631 putative coenzyme Q binding site [chemical binding]; other site 316055007632 Competence-damaged protein; Region: CinA; pfam02464 316055007633 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 316055007634 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 316055007635 substrate binding site; other site 316055007636 dimer interface; other site 316055007637 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 316055007638 homotrimer interaction site [polypeptide binding]; other site 316055007639 zinc binding site [ion binding]; other site 316055007640 CDP-binding sites; other site 316055007641 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 316055007642 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 316055007643 FMN binding site [chemical binding]; other site 316055007644 active site 316055007645 catalytic residues [active] 316055007646 substrate binding site [chemical binding]; other site 316055007647 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 316055007648 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055007649 dimer interface [polypeptide binding]; other site 316055007650 phosphorylation site [posttranslational modification] 316055007651 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 316055007652 ATP binding site [chemical binding]; other site 316055007653 Mg2+ binding site [ion binding]; other site 316055007654 G-X-G motif; other site 316055007655 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 316055007656 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 316055007657 active site 316055007658 phosphorylation site [posttranslational modification] 316055007659 intermolecular recognition site; other site 316055007660 dimerization interface [polypeptide binding]; other site 316055007661 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055007662 Walker A motif; other site 316055007663 ATP binding site [chemical binding]; other site 316055007664 Walker B motif; other site 316055007665 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 316055007666 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 316055007667 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055007668 dimerization interface [polypeptide binding]; other site 316055007669 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 316055007670 putative active site [active] 316055007671 heme pocket [chemical binding]; other site 316055007672 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055007673 dimer interface [polypeptide binding]; other site 316055007674 phosphorylation site [posttranslational modification] 316055007675 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 316055007676 ATP binding site [chemical binding]; other site 316055007677 Mg2+ binding site [ion binding]; other site 316055007678 G-X-G motif; other site 316055007679 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 316055007680 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 316055007681 active site 316055007682 phosphorylation site [posttranslational modification] 316055007683 intermolecular recognition site; other site 316055007684 dimerization interface [polypeptide binding]; other site 316055007685 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055007686 Walker A motif; other site 316055007687 ATP binding site [chemical binding]; other site 316055007688 Walker B motif; other site 316055007689 arginine finger; other site 316055007690 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055007691 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 316055007692 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 316055007693 homodimer interface [polypeptide binding]; other site 316055007694 substrate-cofactor binding pocket; other site 316055007695 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055007696 catalytic residue [active] 316055007697 bacterial Hfq-like; Region: Hfq; cd01716 316055007698 hexamer interface [polypeptide binding]; other site 316055007699 Sm1 motif; other site 316055007700 RNA binding site [nucleotide binding]; other site 316055007701 Sm2 motif; other site 316055007702 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 316055007703 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 316055007704 HflX GTPase family; Region: HflX; cd01878 316055007705 G1 box; other site 316055007706 GTP/Mg2+ binding site [chemical binding]; other site 316055007707 Switch I region; other site 316055007708 G2 box; other site 316055007709 G3 box; other site 316055007710 Switch II region; other site 316055007711 G4 box; other site 316055007712 G5 box; other site 316055007713 DNA gyrase subunit A; Validated; Region: PRK05560 316055007714 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 316055007715 CAP-like domain; other site 316055007716 active site 316055007717 primary dimer interface [polypeptide binding]; other site 316055007718 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316055007719 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316055007720 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316055007721 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316055007722 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316055007723 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 316055007724 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 316055007725 active site 316055007726 (T/H)XGH motif; other site 316055007727 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; cd00317 316055007728 active site 316055007729 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; cd00317 316055007730 active site 316055007731 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 316055007732 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 316055007733 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 316055007734 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 316055007735 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 316055007736 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 316055007737 dimer interface [polypeptide binding]; other site 316055007738 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055007739 catalytic residue [active] 316055007740 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 316055007741 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 316055007742 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 316055007743 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 316055007744 NdvC_like proteins in this family are putative bacterial beta-(1,6)-glucosyltransferase; Region: CESA_NdvC_like; cd06435 316055007745 Ligand binding site; other site 316055007746 DXD motif; other site 316055007747 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 316055007748 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 316055007749 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 316055007750 Substrate binding site; other site 316055007751 Mg++ binding site; other site 316055007752 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 316055007753 active site 316055007754 substrate binding site [chemical binding]; other site 316055007755 CoA binding site [chemical binding]; other site 316055007756 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 316055007757 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 316055007758 glutaminase active site [active] 316055007759 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 316055007760 dimer interface [polypeptide binding]; other site 316055007761 active site 316055007762 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 316055007763 dimer interface [polypeptide binding]; other site 316055007764 active site 316055007765 Uncharacterized conserved protein [Function unknown]; Region: COG2928 316055007766 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 316055007767 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 316055007768 generic binding surface II; other site 316055007769 ssDNA binding site; other site 316055007770 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 316055007771 ATP binding site [chemical binding]; other site 316055007772 putative Mg++ binding site [ion binding]; other site 316055007773 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 316055007774 nucleotide binding region [chemical binding]; other site 316055007775 ATP-binding site [chemical binding]; other site 316055007776 Uncharacterized conserved protein [Function unknown]; Region: COG2938 316055007777 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 316055007778 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 316055007779 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 316055007780 ATP binding site [chemical binding]; other site 316055007781 putative Mg++ binding site [ion binding]; other site 316055007782 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 316055007783 nucleotide binding region [chemical binding]; other site 316055007784 ATP-binding site [chemical binding]; other site 316055007785 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 316055007786 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 316055007787 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055007788 acyl-activating enzyme (AAE) consensus motif; other site 316055007789 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 316055007790 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 316055007791 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 316055007792 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; pfam08755 316055007793 Predicted permeases [General function prediction only]; Region: COG0679 316055007794 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 316055007795 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055007796 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 316055007797 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 316055007798 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 316055007799 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 316055007800 NADP binding site [chemical binding]; other site 316055007801 dimer interface [polypeptide binding]; other site 316055007802 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055007803 AAA domain; Region: AAA_21; pfam13304 316055007804 Walker A/P-loop; other site 316055007805 ATP binding site [chemical binding]; other site 316055007806 Q-loop/lid; other site 316055007807 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055007808 Walker B; other site 316055007809 D-loop; other site 316055007810 H-loop/switch region; other site 316055007811 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 316055007812 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 316055007813 TIR domain; Region: TIR_2; pfam13676 316055007814 short chain dehydrogenase; Provisional; Region: PRK06197 316055007815 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 316055007816 putative NAD(P) binding site [chemical binding]; other site 316055007817 active site 316055007818 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 316055007819 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 316055007820 dimer interface [polypeptide binding]; other site 316055007821 active site 316055007822 glycine-pyridoxal phosphate binding site [chemical binding]; other site 316055007823 folate binding site [chemical binding]; other site 316055007824 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 316055007825 ATP cone domain; Region: ATP-cone; pfam03477 316055007826 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 316055007827 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 316055007828 catalytic motif [active] 316055007829 Zn binding site [ion binding]; other site 316055007830 RibD C-terminal domain; Region: RibD_C; cl17279 316055007831 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 316055007832 Lumazine binding domain; Region: Lum_binding; pfam00677 316055007833 Lumazine binding domain; Region: Lum_binding; pfam00677 316055007834 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 316055007835 homopentamer interface [polypeptide binding]; other site 316055007836 active site 316055007837 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 316055007838 putative RNA binding site [nucleotide binding]; other site 316055007839 thiamine monophosphate kinase; Provisional; Region: PRK05731 316055007840 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 316055007841 ATP binding site [chemical binding]; other site 316055007842 dimerization interface [polypeptide binding]; other site 316055007843 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 316055007844 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 316055007845 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055007846 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055007847 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 316055007848 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 316055007849 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 316055007850 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 316055007851 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 316055007852 dimerization interface [polypeptide binding]; other site 316055007853 Histidine kinase; Region: HisKA_3; pfam07730 316055007854 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 316055007855 ATP binding site [chemical binding]; other site 316055007856 Mg2+ binding site [ion binding]; other site 316055007857 G-X-G motif; other site 316055007858 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055007859 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 316055007860 active site 316055007861 phosphorylation site [posttranslational modification] 316055007862 intermolecular recognition site; other site 316055007863 dimerization interface [polypeptide binding]; other site 316055007864 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055007865 DNA binding residues [nucleotide binding] 316055007866 dimerization interface [polypeptide binding]; other site 316055007867 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 316055007868 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055007869 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 316055007870 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 316055007871 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; pfam03981 316055007872 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 316055007873 putative phosphate acyltransferase; Provisional; Region: PRK05331 316055007874 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 316055007875 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 316055007876 dimer interface [polypeptide binding]; other site 316055007877 active site 316055007878 CoA binding pocket [chemical binding]; other site 316055007879 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 316055007880 IHF dimer interface [polypeptide binding]; other site 316055007881 IHF - DNA interface [nucleotide binding]; other site 316055007882 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 316055007883 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 316055007884 DNA binding residues [nucleotide binding] 316055007885 Uncharacterized conserved protein [Function unknown]; Region: COG2966 316055007886 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 316055007887 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 316055007888 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055007889 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055007890 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055007891 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 316055007892 ligand binding site [chemical binding]; other site 316055007893 flexible hinge region; other site 316055007894 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055007895 non-specific DNA interactions [nucleotide binding]; other site 316055007896 DNA binding site [nucleotide binding] 316055007897 sequence specific DNA binding site [nucleotide binding]; other site 316055007898 putative cAMP binding site [chemical binding]; other site 316055007899 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 316055007900 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055007901 ABC-ATPase subunit interface; other site 316055007902 dimer interface [polypeptide binding]; other site 316055007903 putative PBP binding regions; other site 316055007904 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 316055007905 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055007906 ABC-ATPase subunit interface; other site 316055007907 dimer interface [polypeptide binding]; other site 316055007908 putative PBP binding regions; other site 316055007909 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 316055007910 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 316055007911 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 316055007912 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 316055007913 intersubunit interface [polypeptide binding]; other site 316055007914 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 316055007915 Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane]; Region: WcaJ; COG2148 316055007916 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 316055007917 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055007918 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316055007919 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 316055007920 SLBB domain; Region: SLBB; pfam10531 316055007921 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 316055007922 Chain length determinant protein; Region: Wzz; cl15801 316055007923 AAA domain; Region: AAA_31; pfam13614 316055007924 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 316055007925 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 316055007926 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 316055007927 Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; Region: CE4_Mlr8448_like_5s; cd10968 316055007928 putative active site [active] 316055007929 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 316055007930 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 316055007931 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 316055007932 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 316055007933 CrcB-like protein; Region: CRCB; cl09114 316055007934 camphor resistance protein CrcB; Provisional; Region: PRK14203 316055007935 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK05994 316055007936 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 316055007937 homodimer interface [polypeptide binding]; other site 316055007938 substrate-cofactor binding pocket; other site 316055007939 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055007940 catalytic residue [active] 316055007941 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 316055007942 enoyl-CoA hydratase; Validated; Region: PRK08139 316055007943 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 316055007944 substrate binding site [chemical binding]; other site 316055007945 oxyanion hole (OAH) forming residues; other site 316055007946 trimer interface [polypeptide binding]; other site 316055007947 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 316055007948 CoenzymeA binding site [chemical binding]; other site 316055007949 subunit interaction site [polypeptide binding]; other site 316055007950 PHB binding site; other site 316055007951 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 316055007952 23S rRNA interface [nucleotide binding]; other site 316055007953 L3 interface [polypeptide binding]; other site 316055007954 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 316055007955 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055007956 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055007957 metal binding site [ion binding]; metal-binding site 316055007958 active site 316055007959 I-site; other site 316055007960 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 316055007961 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316055007962 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 316055007963 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 316055007964 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055007965 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055007966 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 316055007967 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 316055007968 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 316055007969 thymidylate kinase; Validated; Region: tmk; PRK00698 316055007970 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 316055007971 TMP-binding site; other site 316055007972 ATP-binding site [chemical binding]; other site 316055007973 DNA polymerase III subunit delta'; Validated; Region: PRK07471 316055007974 DNA polymerase III subunit delta'; Validated; Region: PRK08485 316055007975 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 316055007976 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 316055007977 active site 316055007978 HIGH motif; other site 316055007979 KMSKS motif; other site 316055007980 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 316055007981 tRNA binding surface [nucleotide binding]; other site 316055007982 anticodon binding site; other site 316055007983 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 316055007984 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 316055007985 active site 316055007986 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 316055007987 putative hydrolase; Provisional; Region: PRK02113 316055007988 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055007989 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 316055007990 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 316055007991 dimerization interface [polypeptide binding]; other site 316055007992 D-cysteine desulfhydrase; Validated; Region: PRK03910 316055007993 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 316055007994 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055007995 catalytic residue [active] 316055007996 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 316055007997 putative substrate translocation pore; other site 316055007998 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 316055007999 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_6; cd07242 316055008000 putative dimer interface [polypeptide binding]; other site 316055008001 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055008002 ligand binding site [chemical binding]; other site 316055008003 Zn binding site [ion binding]; other site 316055008004 acyl-CoA synthetase; Validated; Region: PRK08162 316055008005 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 316055008006 acyl-activating enzyme (AAE) consensus motif; other site 316055008007 putative active site [active] 316055008008 AMP binding site [chemical binding]; other site 316055008009 putative CoA binding site [chemical binding]; other site 316055008010 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 316055008011 DctM-like transporters; Region: DctM; pfam06808 316055008012 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 316055008013 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 316055008014 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 316055008015 Sulfatase; Region: Sulfatase; cl17466 316055008016 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 316055008017 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055008018 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 316055008019 dimerization interface [polypeptide binding]; other site 316055008020 substrate binding pocket [chemical binding]; other site 316055008021 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055008022 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 316055008023 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055008024 dimer interface [polypeptide binding]; other site 316055008025 putative CheW interface [polypeptide binding]; other site 316055008026 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055008027 dimerization interface [polypeptide binding]; other site 316055008028 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055008029 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055008030 dimer interface [polypeptide binding]; other site 316055008031 putative CheW interface [polypeptide binding]; other site 316055008032 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 316055008033 Part of AAA domain; Region: AAA_19; pfam13245 316055008034 Family description; Region: UvrD_C_2; pfam13538 316055008035 Putative mono-oxygenase ydhR; Region: ydhR; cl07420 316055008036 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 316055008037 Ligand Binding Site [chemical binding]; other site 316055008038 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 316055008039 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 316055008040 homodimer interface [polypeptide binding]; other site 316055008041 metal binding site [ion binding]; metal-binding site 316055008042 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 316055008043 homodimer interface [polypeptide binding]; other site 316055008044 active site 316055008045 putative chemical substrate binding site [chemical binding]; other site 316055008046 metal binding site [ion binding]; metal-binding site 316055008047 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 316055008048 Domain of unknown function DUF21; Region: DUF21; pfam01595 316055008049 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 316055008050 Transporter associated domain; Region: CorC_HlyC; smart01091 316055008051 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 316055008052 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 316055008053 dimer interface [polypeptide binding]; other site 316055008054 ssDNA binding site [nucleotide binding]; other site 316055008055 tetramer (dimer of dimers) interface [polypeptide binding]; other site 316055008056 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 316055008057 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 316055008058 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 316055008059 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 316055008060 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 316055008061 Protein of unknown function (DUF4101); Region: DUF4101; pfam13355 316055008062 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 316055008063 Ion channel; Region: Ion_trans_2; pfam07885 316055008064 Predicted acetyltransferase [General function prediction only]; Region: COG2388 316055008065 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 316055008066 Predicted integral membrane protein [Function unknown]; Region: COG5473 316055008067 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 316055008068 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 316055008069 Glucose inhibited division protein A; Region: GIDA; pfam01134 316055008070 Squalene/phytoene synthase; Region: SQS_PSY; pfam00494 316055008071 substrate binding pocket [chemical binding]; other site 316055008072 substrate-Mg2+ binding site; other site 316055008073 aspartate-rich region 1; other site 316055008074 aspartate-rich region 2; other site 316055008075 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cd00248 316055008076 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 316055008077 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 316055008078 Protein export membrane protein; Region: SecD_SecF; pfam02355 316055008079 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 316055008080 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 316055008081 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 316055008082 Preprotein translocase subunit; Region: YajC; pfam02699 316055008083 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 316055008084 Protein of unknown function (DUF815); Region: DUF815; pfam05673 316055008085 Walker A motif; other site 316055008086 ATP binding site [chemical binding]; other site 316055008087 Walker B motif; other site 316055008088 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 316055008089 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 316055008090 active site 316055008091 catalytic residues [active] 316055008092 metal binding site [ion binding]; metal-binding site 316055008093 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 316055008094 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055008095 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055008096 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 316055008097 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 316055008098 carboxyltransferase (CT) interaction site; other site 316055008099 biotinylation site [posttranslational modification]; other site 316055008100 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 316055008101 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 316055008102 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 316055008103 OpgC protein; Region: OpgC_C; pfam10129 316055008104 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055008105 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 316055008106 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 316055008107 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055008108 catalytic residue [active] 316055008109 Omptin family; Region: Omptin; cl01886 316055008110 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055008111 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 316055008112 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055008113 DNA-binding site [nucleotide binding]; DNA binding site 316055008114 RNA-binding motif; other site 316055008115 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055008116 DNA-binding site [nucleotide binding]; DNA binding site 316055008117 RNA-binding motif; other site 316055008118 NAD-dependent deacetylase; Provisional; Region: PRK00481 316055008119 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 316055008120 NAD+ binding site [chemical binding]; other site 316055008121 substrate binding site [chemical binding]; other site 316055008122 Zn binding site [ion binding]; other site 316055008123 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055008124 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 316055008125 dimer interface [polypeptide binding]; other site 316055008126 active site 316055008127 metal binding site [ion binding]; metal-binding site 316055008128 glutathione binding site [chemical binding]; other site 316055008129 PilZ domain; Region: PilZ; pfam07238 316055008130 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055008131 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055008132 Short repeat of unknown function (DUF308); Region: DUF308; cl15828 316055008133 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 316055008134 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 316055008135 FeS/SAM binding site; other site 316055008136 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 316055008137 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 316055008138 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 316055008139 motif 1; other site 316055008140 dimer interface [polypeptide binding]; other site 316055008141 active site 316055008142 motif 2; other site 316055008143 motif 3; other site 316055008144 elongation factor P; Validated; Region: PRK00529 316055008145 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 316055008146 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 316055008147 RNA binding site [nucleotide binding]; other site 316055008148 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 316055008149 RNA binding site [nucleotide binding]; other site 316055008150 putative peptidase; Provisional; Region: PRK11649 316055008151 lytic murein transglycosylase; Region: MltB_2; TIGR02283 316055008152 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055008153 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055008154 catalytic residue [active] 316055008155 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055008156 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 316055008157 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 316055008158 DHH family; Region: DHH; pfam01368 316055008159 DHHA1 domain; Region: DHHA1; pfam02272 316055008160 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 316055008161 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 316055008162 motif II; other site 316055008163 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 316055008164 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 316055008165 putative active site [active] 316055008166 homoserine dehydrogenase; Provisional; Region: PRK06349 316055008167 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 316055008168 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 316055008169 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 316055008170 aminotransferase; Validated; Region: PRK09148 316055008171 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 316055008172 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055008173 homodimer interface [polypeptide binding]; other site 316055008174 catalytic residue [active] 316055008175 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 316055008176 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 316055008177 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 316055008178 PAS fold; Region: PAS_7; pfam12860 316055008179 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055008180 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055008181 metal binding site [ion binding]; metal-binding site 316055008182 active site 316055008183 I-site; other site 316055008184 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 316055008185 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055008186 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 316055008187 S-adenosylmethionine binding site [chemical binding]; other site 316055008188 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 316055008189 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 316055008190 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 316055008191 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316055008192 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 316055008193 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 316055008194 Mg2+ binding site [ion binding]; other site 316055008195 G-X-G motif; other site 316055008196 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 316055008197 anchoring element; other site 316055008198 dimer interface [polypeptide binding]; other site 316055008199 ATP binding site [chemical binding]; other site 316055008200 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 316055008201 active site 316055008202 putative metal-binding site [ion binding]; other site 316055008203 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 316055008204 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 316055008205 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 316055008206 Cu(I) binding site [ion binding]; other site 316055008207 Protein of unknown function (DUF461); Region: DUF461; pfam04314 316055008208 Fe2+ transport protein; Region: Iron_transport; pfam10634 316055008209 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 316055008210 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 316055008211 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 316055008212 Caspase domain; Region: Peptidase_C14; pfam00656 316055008213 active site 316055008214 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 316055008215 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 316055008216 N-terminal plug; other site 316055008217 ligand-binding site [chemical binding]; other site 316055008218 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 316055008219 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 316055008220 ATP binding site [chemical binding]; other site 316055008221 Mg++ binding site [ion binding]; other site 316055008222 motif III; other site 316055008223 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 316055008224 nucleotide binding region [chemical binding]; other site 316055008225 ATP-binding site [chemical binding]; other site 316055008226 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055008227 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055008228 metal binding site [ion binding]; metal-binding site 316055008229 active site 316055008230 I-site; other site 316055008231 Transposase domain (DUF772); Region: DUF772; pfam05598 316055008232 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055008233 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 316055008234 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 316055008235 Domain of unknown function DUF59; Region: DUF59; cl00941 316055008236 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 316055008237 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 316055008238 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055008239 catalytic residue [active] 316055008240 FeS assembly protein SufD; Region: sufD; TIGR01981 316055008241 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 316055008242 FeS assembly ATPase SufC; Region: sufC; TIGR01978 316055008243 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 316055008244 Walker A/P-loop; other site 316055008245 ATP binding site [chemical binding]; other site 316055008246 Q-loop/lid; other site 316055008247 ABC transporter signature motif; other site 316055008248 Walker B; other site 316055008249 D-loop; other site 316055008250 H-loop/switch region; other site 316055008251 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 316055008252 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 316055008253 putative ABC transporter; Region: ycf24; CHL00085 316055008254 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 316055008255 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 316055008256 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055008257 catalytic residue [active] 316055008258 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 316055008259 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 316055008260 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 316055008261 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 316055008262 active site 316055008263 HIGH motif; other site 316055008264 dimer interface [polypeptide binding]; other site 316055008265 KMSKS motif; other site 316055008266 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 316055008267 RNA binding surface [nucleotide binding]; other site 316055008268 Protein of unknown function; Region: DUF3971; pfam13116 316055008269 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 316055008270 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 316055008271 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 316055008272 catalytic triad [active] 316055008273 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 316055008274 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 316055008275 Peptidase family M23; Region: Peptidase_M23; pfam01551 316055008276 peptide chain release factor 2; Provisional; Region: PRK07342 316055008277 This domain is found in peptide chain release factors; Region: PCRF; smart00937 316055008278 RF-1 domain; Region: RF-1; pfam00472 316055008279 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 316055008280 Transglycosylase; Region: Transgly; pfam00912 316055008281 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 316055008282 AMIN domain; Region: AMIN; pfam11741 316055008283 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 316055008284 active site 316055008285 metal binding site [ion binding]; metal-binding site 316055008286 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 316055008287 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 316055008288 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 316055008289 aspartate aminotransferase; Provisional; Region: PRK05764 316055008290 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 316055008291 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055008292 homodimer interface [polypeptide binding]; other site 316055008293 catalytic residue [active] 316055008294 Peptidase family M48; Region: Peptidase_M48; cl12018 316055008295 TPR repeat; Region: TPR_11; pfam13414 316055008296 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 316055008297 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 316055008298 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 316055008299 catalytic residues [active] 316055008300 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 316055008301 Dehydroquinase class II; Region: DHquinase_II; pfam01220 316055008302 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 316055008303 trimer interface [polypeptide binding]; other site 316055008304 active site 316055008305 dimer interface [polypeptide binding]; other site 316055008306 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 316055008307 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 316055008308 carboxyltransferase (CT) interaction site; other site 316055008309 biotinylation site [posttranslational modification]; other site 316055008310 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 316055008311 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055008312 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 316055008313 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 316055008314 CHASE3 domain; Region: CHASE3; pfam05227 316055008315 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055008316 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 316055008317 ATP binding site [chemical binding]; other site 316055008318 Mg2+ binding site [ion binding]; other site 316055008319 G-X-G motif; other site 316055008320 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055008321 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 316055008322 active site 316055008323 phosphorylation site [posttranslational modification] 316055008324 intermolecular recognition site; other site 316055008325 dimerization interface [polypeptide binding]; other site 316055008326 Response regulator receiver domain; Region: Response_reg; pfam00072 316055008327 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 316055008328 active site 316055008329 phosphorylation site [posttranslational modification] 316055008330 intermolecular recognition site; other site 316055008331 dimerization interface [polypeptide binding]; other site 316055008332 Histidine kinase; Region: HisKA_2; pfam07568 316055008333 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 316055008334 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 316055008335 ATP binding site [chemical binding]; other site 316055008336 Mg2+ binding site [ion binding]; other site 316055008337 G-X-G motif; other site 316055008338 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055008339 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 316055008340 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 316055008341 FeS/SAM binding site; other site 316055008342 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 316055008343 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; pfam09923 316055008344 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 316055008345 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055008346 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055008347 Protein of unknown function (DUF1211); Region: DUF1211; pfam06736 316055008348 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 316055008349 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055008350 cyclase homology domain; Region: CHD; cd07302 316055008351 nucleotidyl binding site; other site 316055008352 metal binding site [ion binding]; metal-binding site 316055008353 dimer interface [polypeptide binding]; other site 316055008354 FecR protein; Region: FecR; pfam04773 316055008355 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 316055008356 TPR motif; other site 316055008357 binding surface 316055008358 Tetratricopeptide repeat; Region: TPR_9; pfam13371 316055008359 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 316055008360 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055008361 MarR family; Region: MarR_2; cl17246 316055008362 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 316055008363 dimer interface [polypeptide binding]; other site 316055008364 allosteric magnesium binding site [ion binding]; other site 316055008365 active site 316055008366 aspartate-rich active site metal binding site; other site 316055008367 Schiff base residues; other site 316055008368 RDD family; Region: RDD; pfam06271 316055008369 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 316055008370 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 316055008371 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 316055008372 SOUL heme-binding protein; Region: SOUL; pfam04832 316055008373 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055008374 Histidine kinase; Region: HisKA_2; pfam07568 316055008375 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 316055008376 ATP binding site [chemical binding]; other site 316055008377 Mg2+ binding site [ion binding]; other site 316055008378 G-X-G motif; other site 316055008379 manganese transport protein MntH; Reviewed; Region: PRK00701 316055008380 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 316055008381 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 316055008382 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 316055008383 CAP-like domain; other site 316055008384 active site 316055008385 primary dimer interface [polypeptide binding]; other site 316055008386 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 316055008387 Recombination protein O N terminal; Region: RecO_N; pfam11967 316055008388 Recombination protein O C terminal; Region: RecO_C; pfam02565 316055008389 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055008390 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055008391 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055008392 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055008393 dimer interface [polypeptide binding]; other site 316055008394 putative CheW interface [polypeptide binding]; other site 316055008395 GTPase Era; Reviewed; Region: era; PRK00089 316055008396 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 316055008397 G1 box; other site 316055008398 GTP/Mg2+ binding site [chemical binding]; other site 316055008399 Switch I region; other site 316055008400 G2 box; other site 316055008401 Switch II region; other site 316055008402 G3 box; other site 316055008403 G4 box; other site 316055008404 G5 box; other site 316055008405 KH domain; Region: KH_2; pfam07650 316055008406 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 316055008407 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 316055008408 dimerization interface [polypeptide binding]; other site 316055008409 active site 316055008410 metal binding site [ion binding]; metal-binding site 316055008411 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 316055008412 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 316055008413 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 316055008414 Catalytic site [active] 316055008415 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 316055008416 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 316055008417 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 316055008418 active site 316055008419 hydrophilic channel; other site 316055008420 dimerization interface [polypeptide binding]; other site 316055008421 catalytic residues [active] 316055008422 active site lid [active] 316055008423 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 316055008424 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 316055008425 Zn2+ binding site [ion binding]; other site 316055008426 Mg2+ binding site [ion binding]; other site 316055008427 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 316055008428 synthetase active site [active] 316055008429 NTP binding site [chemical binding]; other site 316055008430 metal binding site [ion binding]; metal-binding site 316055008431 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 316055008432 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 316055008433 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 316055008434 LabA_like proteins; Region: LabA; cd10911 316055008435 Uncharacterized conserved protein [Function unknown]; Region: COG1432 316055008436 putative metal binding site [ion binding]; other site 316055008437 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 316055008438 Fe-S cluster binding site [ion binding]; other site 316055008439 DNA binding site [nucleotide binding] 316055008440 active site 316055008441 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 316055008442 SmpB-tmRNA interface; other site 316055008443 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 316055008444 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 316055008445 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 316055008446 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 316055008447 dimer interface [polypeptide binding]; other site 316055008448 active site 316055008449 catalytic residue [active] 316055008450 Predicted transcriptional regulator [Transcription]; Region: COG1959 316055008451 Transcriptional regulator; Region: Rrf2; pfam02082 316055008452 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 316055008453 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 316055008454 hypothetical protein; Validated; Region: PRK08245 316055008455 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 316055008456 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 316055008457 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 316055008458 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 316055008459 putative active site [active] 316055008460 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 316055008461 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 316055008462 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 316055008463 FeS/SAM binding site; other site 316055008464 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 316055008465 Transposase domain (DUF772); Region: DUF772; pfam05598 316055008466 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316055008467 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 316055008468 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 316055008469 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 316055008470 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 316055008471 G1 box; other site 316055008472 putative GEF interaction site [polypeptide binding]; other site 316055008473 GTP/Mg2+ binding site [chemical binding]; other site 316055008474 Switch I region; other site 316055008475 G2 box; other site 316055008476 G3 box; other site 316055008477 Switch II region; other site 316055008478 G4 box; other site 316055008479 G5 box; other site 316055008480 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 316055008481 multidrug efflux system protein; Provisional; Region: PRK11431 316055008482 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 316055008483 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 316055008484 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 316055008485 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 316055008486 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055008487 TM-ABC transporter signature motif; other site 316055008488 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055008489 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 316055008490 TM-ABC transporter signature motif; other site 316055008491 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055008492 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 316055008493 putative ligand binding site [chemical binding]; other site 316055008494 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055008495 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055008496 Walker A/P-loop; other site 316055008497 ATP binding site [chemical binding]; other site 316055008498 Q-loop/lid; other site 316055008499 ABC transporter signature motif; other site 316055008500 Walker B; other site 316055008501 D-loop; other site 316055008502 H-loop/switch region; other site 316055008503 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055008504 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055008505 Walker A/P-loop; other site 316055008506 ATP binding site [chemical binding]; other site 316055008507 Q-loop/lid; other site 316055008508 ABC transporter signature motif; other site 316055008509 Walker B; other site 316055008510 D-loop; other site 316055008511 H-loop/switch region; other site 316055008512 pyruvate kinase; Validated; Region: PRK08187 316055008513 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 316055008514 active site 316055008515 domain interfaces; other site 316055008516 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 316055008517 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 316055008518 ArsC family; Region: ArsC; pfam03960 316055008519 putative catalytic residues [active] 316055008520 phage shock protein A; Region: phageshock_pspA; TIGR02977 316055008521 LemA family; Region: LemA; cl00742 316055008522 Peptidase family M48; Region: Peptidase_M48; cl12018 316055008523 SnoaL-like domain; Region: SnoaL_2; pfam12680 316055008524 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 316055008525 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 316055008526 Hemerythrin-like domain; Region: Hr-like; cd12108 316055008527 Fe binding site [ion binding]; other site 316055008528 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 316055008529 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 316055008530 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 316055008531 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 316055008532 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 316055008533 Cytochrome c; Region: Cytochrom_C; cl11414 316055008534 Cytochrome c; Region: Cytochrom_C; pfam00034 316055008535 bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a...; Region: bact_SoxC_Moco; cd02113 316055008536 Moco binding site; other site 316055008537 metal coordination site [ion binding]; other site 316055008538 dimerization interface [polypeptide binding]; other site 316055008539 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 316055008540 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 316055008541 active site 316055008542 metal binding site [ion binding]; metal-binding site 316055008543 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 316055008544 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 316055008545 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 316055008546 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 316055008547 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 316055008548 Cytochrome c; Region: Cytochrom_C; pfam00034 316055008549 Domain of unknown function (DUF336); Region: DUF336; cl01249 316055008550 SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide...; Region: SoxW; cd02951 316055008551 catalytic residues [active] 316055008552 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 316055008553 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 316055008554 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 316055008555 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 316055008556 dimerization interface [polypeptide binding]; other site 316055008557 putative DNA binding site [nucleotide binding]; other site 316055008558 putative Zn2+ binding site [ion binding]; other site 316055008559 Predicted transporter component [General function prediction only]; Region: COG2391 316055008560 Sulphur transport; Region: Sulf_transp; pfam04143 316055008561 Sulphur transport; Region: Sulf_transp; pfam04143 316055008562 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 316055008563 4Fe-4S binding domain; Region: Fer4_5; pfam12801 316055008564 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 316055008565 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 316055008566 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1); Region: TDT_SLAC1_like; cd09323 316055008567 gating phenylalanine in ion channel; other site 316055008568 Cytochrome C' Region: Cytochrom_C_2; pfam01322 316055008569 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 316055008570 Protein of unknown function (DUF2023); Region: DUF2023; pfam09633 316055008571 flavodoxin FldA; Validated; Region: PRK09267 316055008572 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 316055008573 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 316055008574 dimerization interface [polypeptide binding]; other site 316055008575 DPS ferroxidase diiron center [ion binding]; other site 316055008576 ion pore; other site 316055008577 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 316055008578 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 316055008579 dinuclear metal binding motif [ion binding]; other site 316055008580 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 316055008581 4Fe-4S binding domain; Region: Fer4_5; pfam12801 316055008582 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 316055008583 4Fe-4S binding domain; Region: Fer4_5; pfam12801 316055008584 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 316055008585 nitrous-oxide reductase; Validated; Region: PRK02888 316055008586 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 316055008587 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 316055008588 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 316055008589 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055008590 Walker A/P-loop; other site 316055008591 ATP binding site [chemical binding]; other site 316055008592 Q-loop/lid; other site 316055008593 ABC transporter signature motif; other site 316055008594 Walker B; other site 316055008595 D-loop; other site 316055008596 H-loop/switch region; other site 316055008597 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 316055008598 NosL; Region: NosL; pfam05573 316055008599 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 316055008600 ApbE family; Region: ApbE; pfam02424 316055008601 Pyruvate formate lyase 1; Region: PFL1; cd01678 316055008602 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 316055008603 coenzyme A binding site [chemical binding]; other site 316055008604 active site 316055008605 catalytic residues [active] 316055008606 glycine loop; other site 316055008607 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 316055008608 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 316055008609 FeS/SAM binding site; other site 316055008610 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 316055008611 active site 316055008612 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 316055008613 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 316055008614 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 316055008615 active site 316055008616 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 316055008617 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055008618 Walker A/P-loop; other site 316055008619 ATP binding site [chemical binding]; other site 316055008620 Q-loop/lid; other site 316055008621 ABC transporter signature motif; other site 316055008622 Walker B; other site 316055008623 D-loop; other site 316055008624 H-loop/switch region; other site 316055008625 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 316055008626 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 316055008627 Walker A/P-loop; other site 316055008628 ATP binding site [chemical binding]; other site 316055008629 Q-loop/lid; other site 316055008630 ABC transporter signature motif; other site 316055008631 Walker B; other site 316055008632 D-loop; other site 316055008633 H-loop/switch region; other site 316055008634 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316055008635 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 316055008636 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 316055008637 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; pfam05845 316055008638 Phosphonate metabolism protein PhnG; Region: PhnG; pfam06754 316055008639 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 316055008640 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316055008641 DNA-binding site [nucleotide binding]; DNA binding site 316055008642 UTRA domain; Region: UTRA; pfam07702 316055008643 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 316055008644 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 316055008645 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055008646 dimer interface [polypeptide binding]; other site 316055008647 conserved gate region; other site 316055008648 ABC-ATPase subunit interface; other site 316055008649 phosphonate ABC transporter, periplasmic phosphonate binding protein; Region: PhnD; TIGR03431 316055008650 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 316055008651 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 316055008652 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 316055008653 Walker A/P-loop; other site 316055008654 ATP binding site [chemical binding]; other site 316055008655 Q-loop/lid; other site 316055008656 ABC transporter signature motif; other site 316055008657 Walker B; other site 316055008658 D-loop; other site 316055008659 H-loop/switch region; other site 316055008660 phosphonate metabolim protein, transferase hexapeptide repeat family; Region: phn_thr-fam; TIGR03308 316055008661 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 316055008662 trimer interface [polypeptide binding]; other site 316055008663 active site 316055008664 substrate binding site [chemical binding]; other site 316055008665 CoA binding site [chemical binding]; other site 316055008666 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 316055008667 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 316055008668 active site 316055008669 putative phosphonate metabolism protein; Region: Phn_opern_protn; TIGR03223 316055008670 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 316055008671 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 316055008672 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 316055008673 Switch I; other site 316055008674 Switch II; other site 316055008675 septum formation inhibitor; Reviewed; Region: minC; PRK05177 316055008676 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 316055008677 cobyric acid synthase; Provisional; Region: PRK00784 316055008678 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055008679 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055008680 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 316055008681 catalytic triad [active] 316055008682 cobalamin synthase; Reviewed; Region: cobS; PRK00235 316055008683 Cysteine-rich small domain; Region: zf-like; cl00946 316055008684 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 316055008685 intersubunit interface [polypeptide binding]; other site 316055008686 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 316055008687 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316055008688 Walker A/P-loop; other site 316055008689 ATP binding site [chemical binding]; other site 316055008690 Q-loop/lid; other site 316055008691 ABC transporter signature motif; other site 316055008692 Walker B; other site 316055008693 D-loop; other site 316055008694 H-loop/switch region; other site 316055008695 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055008696 ABC-ATPase subunit interface; other site 316055008697 dimer interface [polypeptide binding]; other site 316055008698 putative PBP binding regions; other site 316055008699 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 316055008700 putative hydrophobic ligand binding site [chemical binding]; other site 316055008701 protein interface [polypeptide binding]; other site 316055008702 gate; other site 316055008703 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 316055008704 metal ion-dependent adhesion site (MIDAS); other site 316055008705 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 316055008706 metal ion-dependent adhesion site (MIDAS); other site 316055008707 Protein of unknown function DUF58; Region: DUF58; pfam01882 316055008708 von Willebrand factor (vWF) type A domain; Region: VWA; smart00327 316055008709 MoxR-like ATPases [General function prediction only]; Region: COG0714 316055008710 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055008711 Walker A motif; other site 316055008712 ATP binding site [chemical binding]; other site 316055008713 Walker B motif; other site 316055008714 arginine finger; other site 316055008715 Methanol dehydrogenase beta subunit; Region: MDH; pfam02315 316055008716 cytochrome c(L), periplasmic; Region: cytochrome_MoxG; TIGR03872 316055008717 methanol oxidation system protein MoxJ; Region: ABC_MoxJ; TIGR03870 316055008718 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055008719 substrate binding pocket [chemical binding]; other site 316055008720 membrane-bound complex binding site; other site 316055008721 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 316055008722 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 316055008723 Trp docking motif [polypeptide binding]; other site 316055008724 dimer interface [polypeptide binding]; other site 316055008725 active site 316055008726 small subunit binding site [polypeptide binding]; other site 316055008727 HAMP domain; Region: HAMP; pfam00672 316055008728 Histidine kinase; Region: HisKA_3; pfam07730 316055008729 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 316055008730 ATP binding site [chemical binding]; other site 316055008731 Mg2+ binding site [ion binding]; other site 316055008732 G-X-G motif; other site 316055008733 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055008734 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 316055008735 active site 316055008736 phosphorylation site [posttranslational modification] 316055008737 intermolecular recognition site; other site 316055008738 dimerization interface [polypeptide binding]; other site 316055008739 dimerization interface [polypeptide binding]; other site 316055008740 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 316055008741 DNA binding residues [nucleotide binding] 316055008742 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316055008743 metal binding site 2 [ion binding]; metal-binding site 316055008744 putative DNA binding helix; other site 316055008745 metal binding site 1 [ion binding]; metal-binding site 316055008746 dimer interface [polypeptide binding]; other site 316055008747 structural Zn2+ binding site [ion binding]; other site 316055008748 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 316055008749 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 316055008750 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 316055008751 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 316055008752 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316055008753 putative heme utilization carrier protein HutX; Region: HutX; TIGR04108 316055008754 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 316055008755 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 316055008756 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 316055008757 N-terminal plug; other site 316055008758 ligand-binding site [chemical binding]; other site 316055008759 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 316055008760 NADH(P)-binding; Region: NAD_binding_10; pfam13460 316055008761 NAD(P) binding site [chemical binding]; other site 316055008762 putative active site [active] 316055008763 coproporphyrinogen III oxidase; Provisional; Region: PRK09058 316055008764 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 316055008765 FeS/SAM binding site; other site 316055008766 Hemin uptake protein hemP; Region: hemP; pfam10636 316055008767 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 316055008768 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 316055008769 putative hemin binding site; other site 316055008770 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 316055008771 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 316055008772 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055008773 ABC-ATPase subunit interface; other site 316055008774 dimer interface [polypeptide binding]; other site 316055008775 putative PBP binding regions; other site 316055008776 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 316055008777 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316055008778 Walker A/P-loop; other site 316055008779 ATP binding site [chemical binding]; other site 316055008780 Q-loop/lid; other site 316055008781 ABC transporter signature motif; other site 316055008782 Walker B; other site 316055008783 D-loop; other site 316055008784 H-loop/switch region; other site 316055008785 Uncharacterized ACR, YagE family COG1723; Region: DUF155; pfam02582 316055008786 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 316055008787 propionate/acetate kinase; Provisional; Region: PRK12379 316055008788 Acetate kinase [Energy production and conversion]; Region: ackA; COG0282 316055008789 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 316055008790 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 316055008791 dimer interaction site [polypeptide binding]; other site 316055008792 substrate-binding tunnel; other site 316055008793 active site 316055008794 catalytic site [active] 316055008795 substrate binding site [chemical binding]; other site 316055008796 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 316055008797 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 316055008798 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055008799 NAD(P) binding site [chemical binding]; other site 316055008800 active site 316055008801 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 316055008802 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055008803 Coenzyme A binding pocket [chemical binding]; other site 316055008804 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 316055008805 ornithine decarboxylase; Provisional; Region: PRK13578 316055008806 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 316055008807 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055008808 catalytic residue [active] 316055008809 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316055008810 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 316055008811 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 316055008812 THF binding site; other site 316055008813 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 316055008814 substrate binding site [chemical binding]; other site 316055008815 THF binding site; other site 316055008816 zinc-binding site [ion binding]; other site 316055008817 Uncharacterized BCR, COG1636; Region: DUF208; pfam02677 316055008818 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 316055008819 active site 316055008820 Mg2+/Mn2+ binding site [ion binding]; other site 316055008821 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 316055008822 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055008823 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 316055008824 non-specific DNA binding site [nucleotide binding]; other site 316055008825 salt bridge; other site 316055008826 sequence-specific DNA binding site [nucleotide binding]; other site 316055008827 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 316055008828 Domain of unknown function (DUF955); Region: DUF955; pfam06114 316055008829 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 316055008830 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 316055008831 FeS/SAM binding site; other site 316055008832 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 316055008833 ATP cone domain; Region: ATP-cone; pfam03477 316055008834 Class III ribonucleotide reductase; Region: RNR_III; cd01675 316055008835 effector binding site; other site 316055008836 active site 316055008837 Zn binding site [ion binding]; other site 316055008838 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 316055008839 diiron center [ion binding]; other site 316055008840 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 316055008841 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 316055008842 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 316055008843 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055008844 acyl-activating enzyme (AAE) consensus motif; other site 316055008845 AMP binding site [chemical binding]; other site 316055008846 active site 316055008847 CoA binding site [chemical binding]; other site 316055008848 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 316055008849 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 316055008850 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055008851 dimer interface [polypeptide binding]; other site 316055008852 conserved gate region; other site 316055008853 ABC-ATPase subunit interface; other site 316055008854 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 316055008855 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 316055008856 Walker A/P-loop; other site 316055008857 ATP binding site [chemical binding]; other site 316055008858 Q-loop/lid; other site 316055008859 ABC transporter signature motif; other site 316055008860 Walker B; other site 316055008861 D-loop; other site 316055008862 H-loop/switch region; other site 316055008863 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316055008864 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 316055008865 serine O-acetyltransferase; Region: cysE; TIGR01172 316055008866 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 316055008867 trimer interface [polypeptide binding]; other site 316055008868 active site 316055008869 substrate binding site [chemical binding]; other site 316055008870 CoA binding site [chemical binding]; other site 316055008871 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 316055008872 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 316055008873 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055008874 catalytic residue [active] 316055008875 Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent...; Region: Nitrogenase_VnfN_like; cd01971 316055008876 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 316055008877 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 316055008878 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 316055008879 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055008880 nitrogenase iron protein; Region: nifH; TIGR01287 316055008881 Radical SAM superfamily; Region: Radical_SAM; pfam04055 316055008882 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 316055008883 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055008884 substrate binding pocket [chemical binding]; other site 316055008885 membrane-bound complex binding site; other site 316055008886 hinge residues; other site 316055008887 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 316055008888 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 316055008889 active site 316055008890 dimer interface [polypeptide binding]; other site 316055008891 non-prolyl cis peptide bond; other site 316055008892 insertion regions; other site 316055008893 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055008894 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055008895 dimer interface [polypeptide binding]; other site 316055008896 conserved gate region; other site 316055008897 putative PBP binding loops; other site 316055008898 ABC-ATPase subunit interface; other site 316055008899 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 316055008900 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055008901 Walker A/P-loop; other site 316055008902 ATP binding site [chemical binding]; other site 316055008903 Q-loop/lid; other site 316055008904 ABC transporter signature motif; other site 316055008905 Walker B; other site 316055008906 D-loop; other site 316055008907 H-loop/switch region; other site 316055008908 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 316055008909 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055008910 UDP-glucose 4 epimerase (G4E), subgroup 3, extended (e) SDRs; Region: UDP_G4E_3_SDR_e; cd05240 316055008911 putative NAD(P) binding site [chemical binding]; other site 316055008912 active site 316055008913 putative substrate binding site [chemical binding]; other site 316055008914 bile acid transporter; Region: bass; TIGR00841 316055008915 Sodium Bile acid symporter family; Region: SBF; cl17470 316055008916 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 316055008917 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 316055008918 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055008919 PYR/PP interface [polypeptide binding]; other site 316055008920 dimer interface [polypeptide binding]; other site 316055008921 TPP binding site [chemical binding]; other site 316055008922 sulfoacetaldehyde acetyltransferase; Validated; Region: PRK07525 316055008923 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055008924 PYR/PP interface [polypeptide binding]; other site 316055008925 dimer interface [polypeptide binding]; other site 316055008926 TPP binding site [chemical binding]; other site 316055008927 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316055008928 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 316055008929 TPP-binding site [chemical binding]; other site 316055008930 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 316055008931 CoA binding domain; Region: CoA_binding; smart00881 316055008932 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 316055008933 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 316055008934 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 316055008935 CoA-ligase; Region: Ligase_CoA; pfam00549 316055008936 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 316055008937 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 316055008938 putative catalytic cysteine [active] 316055008939 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 316055008940 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 316055008941 substrate binding pocket [chemical binding]; other site 316055008942 membrane-bound complex binding site; other site 316055008943 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 316055008944 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055008945 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055008946 Walker A/P-loop; other site 316055008947 ATP binding site [chemical binding]; other site 316055008948 Q-loop/lid; other site 316055008949 ABC transporter signature motif; other site 316055008950 Walker B; other site 316055008951 D-loop; other site 316055008952 H-loop/switch region; other site 316055008953 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055008954 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 316055008955 TM-ABC transporter signature motif; other site 316055008956 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055008957 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055008958 Walker A/P-loop; other site 316055008959 ATP binding site [chemical binding]; other site 316055008960 Q-loop/lid; other site 316055008961 ABC transporter signature motif; other site 316055008962 Walker B; other site 316055008963 D-loop; other site 316055008964 H-loop/switch region; other site 316055008965 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 316055008966 TM-ABC transporter signature motif; other site 316055008967 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316055008968 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055008969 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 316055008970 putative ligand binding site [chemical binding]; other site 316055008971 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 316055008972 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055008973 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316055008974 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055008975 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055008976 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 316055008977 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 316055008978 catalytic loop [active] 316055008979 iron binding site [ion binding]; other site 316055008980 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316055008981 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 316055008982 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 316055008983 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 316055008984 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 316055008985 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 316055008986 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 316055008987 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 316055008988 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 316055008989 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055008990 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055008991 acyl-activating enzyme (AAE) consensus motif; other site 316055008992 acyl-activating enzyme (AAE) consensus motif; other site 316055008993 putative AMP binding site [chemical binding]; other site 316055008994 putative active site [active] 316055008995 putative CoA binding site [chemical binding]; other site 316055008996 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 316055008997 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 316055008998 dimer interface [polypeptide binding]; other site 316055008999 active site 316055009000 Transcriptional regulators [Transcription]; Region: GntR; COG1802 316055009001 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316055009002 DNA-binding site [nucleotide binding]; DNA binding site 316055009003 FCD domain; Region: FCD; pfam07729 316055009004 EthD domain; Region: EthD; cl17553 316055009005 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055009006 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055009007 active site 316055009008 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 316055009009 B12 binding site [chemical binding]; other site 316055009010 cobalt ligand [ion binding]; other site 316055009011 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 316055009012 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 316055009013 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 316055009014 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 316055009015 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 316055009016 substrate binding site [chemical binding]; other site 316055009017 oxyanion hole (OAH) forming residues; other site 316055009018 trimer interface [polypeptide binding]; other site 316055009019 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 316055009020 homotrimer interaction site [polypeptide binding]; other site 316055009021 putative active site [active] 316055009022 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055009023 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 316055009024 acyl-activating enzyme (AAE) consensus motif; other site 316055009025 AMP binding site [chemical binding]; other site 316055009026 active site 316055009027 CoA binding site [chemical binding]; other site 316055009028 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 316055009029 classical (c) SDRs; Region: SDR_c; cd05233 316055009030 NAD(P) binding site [chemical binding]; other site 316055009031 active site 316055009032 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 316055009033 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055009034 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 316055009035 active site 316055009036 FMN binding site [chemical binding]; other site 316055009037 substrate binding site [chemical binding]; other site 316055009038 homotetramer interface [polypeptide binding]; other site 316055009039 catalytic residue [active] 316055009040 MarR family; Region: MarR; pfam01047 316055009041 Sensors of blue-light using FAD; Region: BLUF; pfam04940 316055009042 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 316055009043 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 316055009044 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 316055009045 putative active site [active] 316055009046 Domain of unknown function (DUF4365); Region: DUF4365; pfam14280 316055009047 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 316055009048 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 316055009049 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055009050 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055009051 FecR protein; Region: FecR; pfam04773 316055009052 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 316055009053 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055009054 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055009055 DNA binding residues [nucleotide binding] 316055009056 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055009057 Integrase core domain; Region: rve_3; cl15866 316055009058 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 316055009059 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 316055009060 oligomeric interface; other site 316055009061 putative active site [active] 316055009062 homodimer interface [polypeptide binding]; other site 316055009063 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 316055009064 AIPR protein; Region: AIPR; pfam10592 316055009065 Domain of unknown function (DUF4420); Region: DUF4420; pfam14390 316055009066 Z1 domain; Region: Z1; pfam10593 316055009067 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 316055009068 ATP binding site [chemical binding]; other site 316055009069 Mg2+ binding site [ion binding]; other site 316055009070 G-X-G motif; other site 316055009071 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 316055009072 additional DNA contacts [nucleotide binding]; other site 316055009073 mismatch recognition site; other site 316055009074 active site 316055009075 zinc binding site [ion binding]; other site 316055009076 DNA intercalation site [nucleotide binding]; other site 316055009077 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 316055009078 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 316055009079 cofactor binding site; other site 316055009080 DNA binding site [nucleotide binding] 316055009081 substrate interaction site [chemical binding]; other site 316055009082 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 316055009083 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 316055009084 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 316055009085 Conjugal transfer protein TraD; Region: TraD; pfam06412 316055009086 Conjugal transfer protein TraD; Region: TraD; pfam06412 316055009087 conjugal transfer relaxase TraA; Provisional; Region: PRK13889 316055009088 MobA/MobL family; Region: MobA_MobL; pfam03389 316055009089 AAA domain; Region: AAA_30; pfam13604 316055009090 Family description; Region: UvrD_C_2; pfam13538 316055009091 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 316055009092 integrase; Provisional; Region: PRK09692 316055009093 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 316055009094 active site 316055009095 Int/Topo IB signature motif; other site 316055009096 GMP synthase; Reviewed; Region: guaA; PRK00074 316055009097 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 316055009098 AMP/PPi binding site [chemical binding]; other site 316055009099 candidate oxyanion hole; other site 316055009100 catalytic triad [active] 316055009101 potential glutamine specificity residues [chemical binding]; other site 316055009102 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 316055009103 ATP Binding subdomain [chemical binding]; other site 316055009104 Ligand Binding sites [chemical binding]; other site 316055009105 Dimerization subdomain; other site 316055009106 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 316055009107 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 316055009108 MAPEG family; Region: MAPEG; cl09190 316055009109 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 316055009110 Prostaglandin dehydrogenases; Region: PGDH; cd05288 316055009111 NAD(P) binding site [chemical binding]; other site 316055009112 substrate binding site [chemical binding]; other site 316055009113 dimer interface [polypeptide binding]; other site 316055009114 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 316055009115 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 316055009116 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 316055009117 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 316055009118 active site 316055009119 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 316055009120 putative transporter; Provisional; Region: PRK10504 316055009121 putative substrate translocation pore; other site 316055009122 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 316055009123 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 316055009124 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 316055009125 S-adenosylmethionine binding site [chemical binding]; other site 316055009126 exopolyphosphatase; Region: exo_poly_only; TIGR03706 316055009127 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 316055009128 Predicted membrane protein [Function unknown]; Region: COG2259 316055009129 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 316055009130 Malic enzyme, N-terminal domain; Region: malic; pfam00390 316055009131 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 316055009132 putative NAD(P) binding site [chemical binding]; other site 316055009133 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 316055009134 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 316055009135 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 316055009136 dimer interface [polypeptide binding]; other site 316055009137 anticodon binding site; other site 316055009138 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 316055009139 homodimer interface [polypeptide binding]; other site 316055009140 motif 1; other site 316055009141 active site 316055009142 motif 2; other site 316055009143 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 316055009144 active site 316055009145 motif 3; other site 316055009146 hypothetical protein; Validated; Region: PRK00029 316055009147 Uncharacterized conserved protein [Function unknown]; Region: COG0397 316055009148 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 316055009149 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 316055009150 catalytic site [active] 316055009151 putative active site [active] 316055009152 putative substrate binding site [chemical binding]; other site 316055009153 HRDC domain; Region: HRDC; pfam00570 316055009154 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 316055009155 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 316055009156 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 316055009157 polyphosphate kinase; Provisional; Region: PRK05443 316055009158 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 316055009159 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 316055009160 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 316055009161 putative domain interface [polypeptide binding]; other site 316055009162 putative active site [active] 316055009163 catalytic site [active] 316055009164 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 316055009165 putative domain interface [polypeptide binding]; other site 316055009166 putative active site [active] 316055009167 catalytic site [active] 316055009168 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 316055009169 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 316055009170 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 316055009171 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 316055009172 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 316055009173 dimerization interface [polypeptide binding]; other site 316055009174 putative ATP binding site [chemical binding]; other site 316055009175 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 316055009176 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 316055009177 active site 316055009178 substrate binding site [chemical binding]; other site 316055009179 cosubstrate binding site; other site 316055009180 catalytic site [active] 316055009181 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055009182 DNA-binding site [nucleotide binding]; DNA binding site 316055009183 RNA-binding motif; other site 316055009184 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 316055009185 active site 316055009186 multimer interface [polypeptide binding]; other site 316055009187 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 316055009188 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055009189 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055009190 ABC transporter; Region: ABC_tran_2; pfam12848 316055009191 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 316055009192 DNA polymerase III subunit chi; Validated; Region: PRK05728 316055009193 multifunctional aminopeptidase A; Provisional; Region: PRK00913 316055009194 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 316055009195 interface (dimer of trimers) [polypeptide binding]; other site 316055009196 Substrate-binding/catalytic site; other site 316055009197 Zn-binding sites [ion binding]; other site 316055009198 Predicted permeases [General function prediction only]; Region: COG0795 316055009199 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 316055009200 Predicted permeases [General function prediction only]; Region: COG0795 316055009201 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 316055009202 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 316055009203 OstA-like protein; Region: OstA; cl00844 316055009204 Organic solvent tolerance protein; Region: OstA_C; pfam04453 316055009205 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 316055009206 SurA N-terminal domain; Region: SurA_N; pfam09312 316055009207 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK05312 316055009208 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 316055009209 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 316055009210 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 316055009211 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 316055009212 6-hydroxyhexanoate dehydrogenase; Region: 6_hydroxyhexanoate_dh_like; cd08240 316055009213 putative NAD(P) binding site [chemical binding]; other site 316055009214 catalytic Zn binding site [ion binding]; other site 316055009215 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 316055009216 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 316055009217 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 316055009218 catalytic site [active] 316055009219 G-X2-G-X-G-K; other site 316055009220 hypothetical protein; Provisional; Region: PRK11820 316055009221 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 316055009222 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 316055009223 YceG-like family; Region: YceG; pfam02618 316055009224 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 316055009225 dimerization interface [polypeptide binding]; other site 316055009226 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 316055009227 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 316055009228 dimer interface [polypeptide binding]; other site 316055009229 active site 316055009230 acyl carrier protein; Provisional; Region: acpP; PRK00982 316055009231 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed; Region: PRK12936 316055009232 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055009233 NAD(P) binding site [chemical binding]; other site 316055009234 active site 316055009235 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 316055009236 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 316055009237 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055009238 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055009239 metal binding site [ion binding]; metal-binding site 316055009240 active site 316055009241 I-site; other site 316055009242 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 316055009243 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 316055009244 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; cl17861 316055009245 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 316055009246 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 316055009247 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 316055009248 replicative DNA helicase; Provisional; Region: PRK09165 316055009249 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 316055009250 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 316055009251 Walker A motif; other site 316055009252 ATP binding site [chemical binding]; other site 316055009253 Walker B motif; other site 316055009254 DNA binding loops [nucleotide binding] 316055009255 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055009256 Walker A/P-loop; other site 316055009257 ATP binding site [chemical binding]; other site 316055009258 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055009259 DevC protein; Region: devC; TIGR01185 316055009260 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 316055009261 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055009262 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055009263 Walker A/P-loop; other site 316055009264 ATP binding site [chemical binding]; other site 316055009265 Q-loop/lid; other site 316055009266 ABC transporter signature motif; other site 316055009267 Walker B; other site 316055009268 D-loop; other site 316055009269 H-loop/switch region; other site 316055009270 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 316055009271 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 316055009272 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055009273 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 316055009274 dimerization interface [polypeptide binding]; other site 316055009275 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055009276 dimer interface [polypeptide binding]; other site 316055009277 phosphorylation site [posttranslational modification] 316055009278 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 316055009279 ATP binding site [chemical binding]; other site 316055009280 Mg2+ binding site [ion binding]; other site 316055009281 G-X-G motif; other site 316055009282 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055009283 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 316055009284 active site 316055009285 phosphorylation site [posttranslational modification] 316055009286 intermolecular recognition site; other site 316055009287 dimerization interface [polypeptide binding]; other site 316055009288 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055009289 DNA binding site [nucleotide binding] 316055009290 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 316055009291 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055009292 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055009293 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 316055009294 Protein export membrane protein; Region: SecD_SecF; cl14618 316055009295 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 316055009296 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 316055009297 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055009298 Coenzyme A binding pocket [chemical binding]; other site 316055009299 PAS fold; Region: PAS_7; pfam12860 316055009300 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055009301 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055009302 metal binding site [ion binding]; metal-binding site 316055009303 active site 316055009304 I-site; other site 316055009305 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 316055009306 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 316055009307 active site 316055009308 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 316055009309 dimer interface [polypeptide binding]; other site 316055009310 substrate binding site [chemical binding]; other site 316055009311 catalytic residues [active] 316055009312 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055009313 Coenzyme A binding pocket [chemical binding]; other site 316055009314 DNA repair protein RadA; Provisional; Region: PRK11823 316055009315 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055009316 Walker A motif; other site 316055009317 ATP binding site [chemical binding]; other site 316055009318 Walker B motif; other site 316055009319 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 316055009320 Colicin V production protein; Region: Colicin_V; pfam02674 316055009321 amidophosphoribosyltransferase; Provisional; Region: PRK09123 316055009322 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 316055009323 active site 316055009324 tetramer interface [polypeptide binding]; other site 316055009325 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055009326 active site 316055009327 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 316055009328 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055009329 NAD(P) binding site [chemical binding]; other site 316055009330 active site 316055009331 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 316055009332 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 316055009333 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055009334 putative substrate translocation pore; other site 316055009335 GTP-binding protein Der; Reviewed; Region: PRK00093 316055009336 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 316055009337 G1 box; other site 316055009338 GTP/Mg2+ binding site [chemical binding]; other site 316055009339 Switch I region; other site 316055009340 G2 box; other site 316055009341 Switch II region; other site 316055009342 G3 box; other site 316055009343 G4 box; other site 316055009344 G5 box; other site 316055009345 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 316055009346 G1 box; other site 316055009347 GTP/Mg2+ binding site [chemical binding]; other site 316055009348 Switch I region; other site 316055009349 G2 box; other site 316055009350 G3 box; other site 316055009351 Switch II region; other site 316055009352 G4 box; other site 316055009353 G5 box; other site 316055009354 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 316055009355 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 316055009356 Uncharacterized protein family (UPF0253); Region: UPF0253; cl11640 316055009357 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 316055009358 oligomerization interface [polypeptide binding]; other site 316055009359 active site 316055009360 metal binding site [ion binding]; metal-binding site 316055009361 NnrU protein; Region: NnrU; pfam07298 316055009362 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 316055009363 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316055009364 Sel1 repeat; Region: Sel1; cl02723 316055009365 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 316055009366 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 316055009367 GatB domain; Region: GatB_Yqey; smart00845 316055009368 Patatin-like phospholipase; Region: Patatin; pfam01734 316055009369 active site 316055009370 nucleophile elbow; other site 316055009371 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 316055009372 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 316055009373 Protein of unknown function (DUF497); Region: DUF497; pfam04365 316055009374 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 316055009375 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 316055009376 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 316055009377 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 316055009378 FMN binding site [chemical binding]; other site 316055009379 substrate binding site [chemical binding]; other site 316055009380 putative catalytic residue [active] 316055009381 Putative cyclase; Region: Cyclase; pfam04199 316055009382 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055009383 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055009384 myosin-cross-reactive antigen; Provisional; Region: PRK13977 316055009385 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 316055009386 Predicted permeases [General function prediction only]; Region: COG0679 316055009387 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 316055009388 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 316055009389 ligand binding site [chemical binding]; other site 316055009390 flexible hinge region; other site 316055009391 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055009392 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055009393 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 316055009394 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055009395 non-specific DNA interactions [nucleotide binding]; other site 316055009396 DNA binding site [nucleotide binding] 316055009397 sequence specific DNA binding site [nucleotide binding]; other site 316055009398 putative cAMP binding site [chemical binding]; other site 316055009399 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 316055009400 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 316055009401 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316055009402 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316055009403 dihydroorotase; Validated; Region: PRK09059 316055009404 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 316055009405 active site 316055009406 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 316055009407 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 316055009408 DNA protecting protein DprA; Region: dprA; TIGR00732 316055009409 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 316055009410 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 316055009411 active site 316055009412 interdomain interaction site; other site 316055009413 putative metal-binding site [ion binding]; other site 316055009414 nucleotide binding site [chemical binding]; other site 316055009415 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 316055009416 domain I; other site 316055009417 DNA binding groove [nucleotide binding] 316055009418 phosphate binding site [ion binding]; other site 316055009419 domain II; other site 316055009420 domain III; other site 316055009421 nucleotide binding site [chemical binding]; other site 316055009422 catalytic site [active] 316055009423 domain IV; other site 316055009424 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 316055009425 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 316055009426 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 316055009427 ribonuclease R; Region: RNase_R; TIGR02063 316055009428 RNB domain; Region: RNB; pfam00773 316055009429 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 316055009430 RNA binding site [nucleotide binding]; other site 316055009431 hypothetical protein; Provisional; Region: PRK05978 316055009432 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 316055009433 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055009434 response regulator PleD; Reviewed; Region: pleD; PRK09581 316055009435 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 316055009436 active site 316055009437 phosphorylation site [posttranslational modification] 316055009438 intermolecular recognition site; other site 316055009439 dimerization interface [polypeptide binding]; other site 316055009440 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 316055009441 active site 316055009442 phosphorylation site [posttranslational modification] 316055009443 intermolecular recognition site; other site 316055009444 dimerization interface [polypeptide binding]; other site 316055009445 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055009446 metal binding site [ion binding]; metal-binding site 316055009447 active site 316055009448 I-site; other site 316055009449 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055009450 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 316055009451 active site 316055009452 phosphorylation site [posttranslational modification] 316055009453 intermolecular recognition site; other site 316055009454 dimerization interface [polypeptide binding]; other site 316055009455 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 316055009456 DNA polymerase IV; Provisional; Region: PRK02794 316055009457 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 316055009458 active site 316055009459 DNA binding site [nucleotide binding] 316055009460 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 316055009461 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 316055009462 homotrimer interaction site [polypeptide binding]; other site 316055009463 putative active site [active] 316055009464 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_3; cd08585 316055009465 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 316055009466 putative active site [active] 316055009467 catalytic site [active] 316055009468 putative metal binding site [ion binding]; other site 316055009469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3146 316055009470 Protein of unknown function, DUF482; Region: DUF482; pfam04339 316055009471 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 316055009472 HIT family signature motif; other site 316055009473 catalytic residue [active] 316055009474 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 316055009475 homodimer interaction site [polypeptide binding]; other site 316055009476 cofactor binding site; other site 316055009477 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 316055009478 AzlC protein; Region: AzlC; cl00570 316055009479 PilZ domain; Region: PilZ; pfam07238 316055009480 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 316055009481 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055009482 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055009483 catalytic residue [active] 316055009484 Sporulation related domain; Region: SPOR; pfam05036 316055009485 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 316055009486 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 316055009487 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055009488 catalytic residue [active] 316055009489 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 316055009490 AAA domain; Region: AAA_26; pfam13500 316055009491 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 316055009492 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 316055009493 inhibitor-cofactor binding pocket; inhibition site 316055009494 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055009495 catalytic residue [active] 316055009496 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 316055009497 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 316055009498 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055009499 Walker A motif; other site 316055009500 ATP binding site [chemical binding]; other site 316055009501 Walker B motif; other site 316055009502 arginine finger; other site 316055009503 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055009504 Walker A motif; other site 316055009505 ATP binding site [chemical binding]; other site 316055009506 Walker B motif; other site 316055009507 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 316055009508 Uncharacterized conserved protein [Function unknown]; Region: COG2127 316055009509 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 316055009510 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 316055009511 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 316055009512 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 316055009513 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 316055009514 Sporulation related domain; Region: SPOR; pfam05036 316055009515 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 316055009516 HSP70 interaction site [polypeptide binding]; other site 316055009517 von Willebrand factor type A domain; Region: VWA_2; pfam13519 316055009518 mobile mystery protein B; Region: mob_myst_B; TIGR02613 316055009519 Fic/DOC family; Region: Fic; pfam02661 316055009520 mobile mystery protein A; Region: mob_myst_A; TIGR02612 316055009521 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 316055009522 non-specific DNA binding site [nucleotide binding]; other site 316055009523 salt bridge; other site 316055009524 sequence-specific DNA binding site [nucleotide binding]; other site 316055009525 ATPase MipZ; Region: MipZ; pfam09140 316055009526 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055009527 P-loop; other site 316055009528 Magnesium ion binding site [ion binding]; other site 316055009529 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055009530 Magnesium ion binding site [ion binding]; other site 316055009531 Pantoate-beta-alanine ligase; Region: PanC; cd00560 316055009532 pantoate--beta-alanine ligase; Region: panC; TIGR00018 316055009533 active site 316055009534 ATP-binding site [chemical binding]; other site 316055009535 pantoate-binding site; other site 316055009536 HXXH motif; other site 316055009537 Protein of unknown function (DUF1489); Region: DUF1489; pfam07370 316055009538 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 316055009539 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055009540 putative C-terminal domain interface [polypeptide binding]; other site 316055009541 putative GSH binding site (G-site) [chemical binding]; other site 316055009542 putative dimer interface [polypeptide binding]; other site 316055009543 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 316055009544 putative N-terminal domain interface [polypeptide binding]; other site 316055009545 putative dimer interface [polypeptide binding]; other site 316055009546 putative substrate binding pocket (H-site) [chemical binding]; other site 316055009547 Protein of unknown function (DUF3253); Region: DUF3253; pfam11625 316055009548 Uncharacterized conserved protein [Function unknown]; Region: COG1434 316055009549 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 316055009550 putative active site [active] 316055009551 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 316055009552 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 316055009553 active site 316055009554 catalytic tetrad [active] 316055009555 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 316055009556 non-specific DNA binding site [nucleotide binding]; other site 316055009557 salt bridge; other site 316055009558 sequence-specific DNA binding site [nucleotide binding]; other site 316055009559 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 316055009560 MgtE intracellular N domain; Region: MgtE_N; smart00924 316055009561 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 316055009562 Divalent cation transporter; Region: MgtE; cl00786 316055009563 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 316055009564 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 316055009565 NodB motif; other site 316055009566 active site 316055009567 catalytic site [active] 316055009568 metal binding site [ion binding]; metal-binding site 316055009569 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 316055009570 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 316055009571 NodB motif; other site 316055009572 active site 316055009573 catalytic site [active] 316055009574 metal binding site [ion binding]; metal-binding site 316055009575 Serine hydrolase; Region: Ser_hydrolase; pfam06821 316055009576 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055009577 Citrate lyase synthetase [Energy production and conversion]; Region: CitC; COG3053 316055009578 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 316055009579 putative active site [active] 316055009580 (T/H)XGH motif; other site 316055009581 citrate lyase subunit gamma; Provisional; Region: PRK13253 316055009582 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 316055009583 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 316055009584 Coenzyme A transferase; Region: CoA_trans; cl17247 316055009585 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; Region: CitX; pfam03802 316055009586 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 316055009587 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 316055009588 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 316055009589 oligomeric interface; other site 316055009590 putative active site [active] 316055009591 homodimer interface [polypeptide binding]; other site 316055009592 hypothetical protein; Validated; Region: PRK06033 316055009593 lipoate-protein ligase B; Provisional; Region: PRK14341 316055009594 acylphosphatase; Provisional; Region: PRK14421 316055009595 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 316055009596 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 316055009597 tetramer interface [polypeptide binding]; other site 316055009598 active site 316055009599 Mg2+/Mn2+ binding site [ion binding]; other site 316055009600 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 316055009601 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055009602 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 316055009603 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 316055009604 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 316055009605 carboxyltransferase (CT) interaction site; other site 316055009606 biotinylation site [posttranslational modification]; other site 316055009607 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 316055009608 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 316055009609 DNA photolyase; Region: DNA_photolyase; pfam00875 316055009610 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 316055009611 EamA-like transporter family; Region: EamA; pfam00892 316055009612 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055009613 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055009614 metal binding site [ion binding]; metal-binding site 316055009615 active site 316055009616 I-site; other site 316055009617 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055009618 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055009619 dimer interface [polypeptide binding]; other site 316055009620 phosphorylation site [posttranslational modification] 316055009621 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 316055009622 ATP binding site [chemical binding]; other site 316055009623 Mg2+ binding site [ion binding]; other site 316055009624 G-X-G motif; other site 316055009625 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055009626 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 316055009627 active site 316055009628 phosphorylation site [posttranslational modification] 316055009629 intermolecular recognition site; other site 316055009630 dimerization interface [polypeptide binding]; other site 316055009631 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055009632 DNA binding site [nucleotide binding] 316055009633 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 316055009634 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316055009635 putative active site [active] 316055009636 putative metal binding site [ion binding]; other site 316055009637 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 316055009638 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 316055009639 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055009640 S-adenosylmethionine binding site [chemical binding]; other site 316055009641 Response regulator receiver domain; Region: Response_reg; pfam00072 316055009642 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 316055009643 active site 316055009644 phosphorylation site [posttranslational modification] 316055009645 intermolecular recognition site; other site 316055009646 dimerization interface [polypeptide binding]; other site 316055009647 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 316055009648 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055009649 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055009650 catalytic residue [active] 316055009651 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 316055009652 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 316055009653 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 316055009654 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316055009655 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 316055009656 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 316055009657 Domain of unknown function (DUF2341); Region: DUF2341; pfam10102 316055009658 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 316055009659 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 316055009660 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 316055009661 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 316055009662 Surface antigen; Region: Bac_surface_Ag; pfam01103 316055009663 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055009664 FecR protein; Region: FecR; pfam04773 316055009665 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 316055009666 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 316055009667 DNA binding residues [nucleotide binding] 316055009668 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 316055009669 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 316055009670 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055009671 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316055009672 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 316055009673 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055009674 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 316055009675 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055009676 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055009677 FecR protein; Region: FecR; pfam04773 316055009678 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 316055009679 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055009680 DNA binding residues [nucleotide binding] 316055009681 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316055009682 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055009683 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055009684 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055009685 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055009686 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055009687 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 316055009688 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 316055009689 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 316055009690 N-terminal plug; other site 316055009691 ligand-binding site [chemical binding]; other site 316055009692 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 316055009693 homodimer interaction site [polypeptide binding]; other site 316055009694 cofactor binding site; other site 316055009695 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 316055009696 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 316055009697 putative metal binding site [ion binding]; other site 316055009698 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 316055009699 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055009700 ABC-ATPase subunit interface; other site 316055009701 dimer interface [polypeptide binding]; other site 316055009702 putative PBP binding regions; other site 316055009703 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 316055009704 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316055009705 Walker A/P-loop; other site 316055009706 ATP binding site [chemical binding]; other site 316055009707 Q-loop/lid; other site 316055009708 ABC transporter signature motif; other site 316055009709 Walker B; other site 316055009710 D-loop; other site 316055009711 H-loop/switch region; other site 316055009712 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 316055009713 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 316055009714 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 316055009715 TOBE domain; Region: TOBE; cl01440 316055009716 TOBE domain; Region: TOBE; cl01440 316055009717 Right handed beta helix region; Region: Beta_helix; pfam13229 316055009718 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 316055009719 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 316055009720 active site 316055009721 substrate binding site [chemical binding]; other site 316055009722 metal binding site [ion binding]; metal-binding site 316055009723 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 316055009724 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 316055009725 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 316055009726 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 316055009727 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055009728 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 316055009729 NAD binding site [chemical binding]; other site 316055009730 putative substrate binding site 2 [chemical binding]; other site 316055009731 putative substrate binding site 1 [chemical binding]; other site 316055009732 active site 316055009733 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316055009734 SLBB domain; Region: SLBB; pfam10531 316055009735 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 316055009736 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 316055009737 Substrate binding site; other site 316055009738 Cupin domain; Region: Cupin_2; cl17218 316055009739 Chain length determinant protein; Region: Wzz; cl15801 316055009740 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 316055009741 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055009742 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cd12082 316055009743 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 316055009744 Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)-like, extended (e) SDRs; Region: GME-like_SDR_e; cd05273 316055009745 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055009746 NAD binding site [chemical binding]; other site 316055009747 homodimer interface [polypeptide binding]; other site 316055009748 substrate binding site [chemical binding]; other site 316055009749 active site 316055009750 Bacterial sugar transferase; Region: Bac_transf; pfam02397 316055009751 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 316055009752 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 316055009753 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316055009754 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 316055009755 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055009756 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055009757 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 316055009758 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055009759 NAD(P) binding site [chemical binding]; other site 316055009760 active site 316055009761 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 316055009762 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055009763 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 316055009764 metal-binding site 316055009765 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 316055009766 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055009767 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 316055009768 Walker A/P-loop; other site 316055009769 ATP binding site [chemical binding]; other site 316055009770 Q-loop/lid; other site 316055009771 ABC transporter signature motif; other site 316055009772 Walker B; other site 316055009773 D-loop; other site 316055009774 H-loop/switch region; other site 316055009775 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 316055009776 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055009777 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055009778 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 316055009779 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055009780 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055009781 DNA binding residues [nucleotide binding] 316055009782 dimerization interface [polypeptide binding]; other site 316055009783 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 316055009784 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055009785 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 316055009786 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055009787 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055009788 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 316055009789 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055009790 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316055009791 Transposase; Region: HTH_Tnp_1; pfam01527 316055009792 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055009793 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055009794 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055009795 dimer interface [polypeptide binding]; other site 316055009796 putative CheW interface [polypeptide binding]; other site 316055009797 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055009798 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055009799 dimerization interface [polypeptide binding]; other site 316055009800 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055009801 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055009802 dimer interface [polypeptide binding]; other site 316055009803 putative CheW interface [polypeptide binding]; other site 316055009804 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 316055009805 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055009806 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055009807 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 316055009808 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055009809 putative active site [active] 316055009810 heme pocket [chemical binding]; other site 316055009811 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 316055009812 putative active site [active] 316055009813 heme pocket [chemical binding]; other site 316055009814 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055009815 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 316055009816 ATP binding site [chemical binding]; other site 316055009817 Mg2+ binding site [ion binding]; other site 316055009818 G-X-G motif; other site 316055009819 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 316055009820 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 316055009821 Trp docking motif [polypeptide binding]; other site 316055009822 cytochrome domain interface [polypeptide binding]; other site 316055009823 active site 316055009824 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 316055009825 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 316055009826 nudix motif; other site 316055009827 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 316055009828 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 316055009829 inhibitor site; inhibition site 316055009830 active site 316055009831 dimer interface [polypeptide binding]; other site 316055009832 catalytic residue [active] 316055009833 enoyl-CoA hydratase; Region: PLN02864 316055009834 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 316055009835 HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit; Region: HDE_HSD; cd03448 316055009836 dimer interaction site [polypeptide binding]; other site 316055009837 substrate-binding tunnel; other site 316055009838 active site 316055009839 catalytic site [active] 316055009840 substrate binding site [chemical binding]; other site 316055009841 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 316055009842 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 316055009843 dimer interface [polypeptide binding]; other site 316055009844 PYR/PP interface [polypeptide binding]; other site 316055009845 TPP binding site [chemical binding]; other site 316055009846 substrate binding site [chemical binding]; other site 316055009847 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 316055009848 TPP-binding site [chemical binding]; other site 316055009849 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 316055009850 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 316055009851 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055009852 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 316055009853 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 316055009854 active site 316055009855 substrate binding site [chemical binding]; other site 316055009856 Mg2+ binding site [ion binding]; other site 316055009857 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins; Region: GDPD_EcGlpQ_like_1; cd08560 316055009858 putative active site [active] 316055009859 catalytic site [active] 316055009860 putative metal binding site [ion binding]; other site 316055009861 Cytotoxic; Region: Cytotoxic; pfam09000 316055009862 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 316055009863 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 316055009864 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 316055009865 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 316055009866 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 316055009867 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 316055009868 ATP12 chaperone protein; Region: ATP12; cl02228 316055009869 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 316055009870 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 316055009871 RNA binding surface [nucleotide binding]; other site 316055009872 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 316055009873 active site 316055009874 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 316055009875 putative active site [active] 316055009876 putative NTP binding site [chemical binding]; other site 316055009877 putative nucleic acid binding site [nucleotide binding]; other site 316055009878 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 316055009879 FMN binding site [chemical binding]; other site 316055009880 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 source...; Region: Nitroreductase; cd02136 316055009881 putative FMN binding site [chemical binding]; other site 316055009882 Sensors of blue-light using FAD; Region: BLUF; pfam04940 316055009883 Methyltransferase domain; Region: Methyltransf_31; pfam13847 316055009884 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 316055009885 S-adenosylmethionine binding site [chemical binding]; other site 316055009886 Uncharacterized conserved protein [Function unknown]; Region: COG0432 316055009887 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 316055009888 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 316055009889 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055009890 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055009891 putative ligand binding site [chemical binding]; other site 316055009892 recombination factor protein RarA; Reviewed; Region: PRK13342 316055009893 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055009894 Walker A motif; other site 316055009895 ATP binding site [chemical binding]; other site 316055009896 Walker B motif; other site 316055009897 arginine finger; other site 316055009898 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 316055009899 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 316055009900 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055009901 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055009902 protein binding site [polypeptide binding]; other site 316055009903 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055009904 protein binding site [polypeptide binding]; other site 316055009905 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 316055009906 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 316055009907 putative NAD(P) binding site [chemical binding]; other site 316055009908 dimer interface [polypeptide binding]; other site 316055009909 Uncharacterized conserved protein [Function unknown]; Region: COG3791 316055009910 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 316055009911 classical (c) SDRs; Region: SDR_c; cd05233 316055009912 NAD(P) binding site [chemical binding]; other site 316055009913 active site 316055009914 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 316055009915 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 316055009916 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 316055009917 alphaNTD - beta interaction site [polypeptide binding]; other site 316055009918 alphaNTD homodimer interface [polypeptide binding]; other site 316055009919 alphaNTD - beta' interaction site [polypeptide binding]; other site 316055009920 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 316055009921 30S ribosomal protein S11; Validated; Region: PRK05309 316055009922 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 316055009923 30S ribosomal protein S13; Region: bact_S13; TIGR03631 316055009924 adenylate kinase; Reviewed; Region: adk; PRK00279 316055009925 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 316055009926 AMP-binding site [chemical binding]; other site 316055009927 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 316055009928 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 316055009929 SecY translocase; Region: SecY; pfam00344 316055009930 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 316055009931 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 316055009932 23S rRNA binding site [nucleotide binding]; other site 316055009933 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 316055009934 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 316055009935 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 316055009936 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 316055009937 5S rRNA interface [nucleotide binding]; other site 316055009938 23S rRNA interface [nucleotide binding]; other site 316055009939 L5 interface [polypeptide binding]; other site 316055009940 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 316055009941 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 316055009942 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 316055009943 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 316055009944 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 316055009945 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 316055009946 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 316055009947 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 316055009948 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 316055009949 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 316055009950 RNA binding site [nucleotide binding]; other site 316055009951 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 316055009952 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 316055009953 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 316055009954 putative translocon interaction site; other site 316055009955 23S rRNA interface [nucleotide binding]; other site 316055009956 signal recognition particle (SRP54) interaction site; other site 316055009957 L23 interface [polypeptide binding]; other site 316055009958 trigger factor interaction site; other site 316055009959 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 316055009960 23S rRNA interface [nucleotide binding]; other site 316055009961 5S rRNA interface [nucleotide binding]; other site 316055009962 putative antibiotic binding site [chemical binding]; other site 316055009963 L25 interface [polypeptide binding]; other site 316055009964 L27 interface [polypeptide binding]; other site 316055009965 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 316055009966 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 316055009967 G-X-X-G motif; other site 316055009968 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 316055009969 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 316055009970 putative translocon binding site; other site 316055009971 protein-rRNA interface [nucleotide binding]; other site 316055009972 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 316055009973 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 316055009974 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 316055009975 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 316055009976 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 316055009977 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 316055009978 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 316055009979 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 316055009980 elongation factor Tu; Reviewed; Region: PRK00049 316055009981 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 316055009982 G1 box; other site 316055009983 GEF interaction site [polypeptide binding]; other site 316055009984 GTP/Mg2+ binding site [chemical binding]; other site 316055009985 Switch I region; other site 316055009986 G2 box; other site 316055009987 G3 box; other site 316055009988 Switch II region; other site 316055009989 G4 box; other site 316055009990 G5 box; other site 316055009991 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 316055009992 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 316055009993 Antibiotic Binding Site [chemical binding]; other site 316055009994 elongation factor G; Reviewed; Region: PRK00007 316055009995 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 316055009996 G1 box; other site 316055009997 putative GEF interaction site [polypeptide binding]; other site 316055009998 GTP/Mg2+ binding site [chemical binding]; other site 316055009999 Switch I region; other site 316055010000 G2 box; other site 316055010001 G3 box; other site 316055010002 Switch II region; other site 316055010003 G4 box; other site 316055010004 G5 box; other site 316055010005 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 316055010006 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 316055010007 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 316055010008 30S ribosomal protein S7; Validated; Region: PRK05302 316055010009 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 316055010010 S17 interaction site [polypeptide binding]; other site 316055010011 S8 interaction site; other site 316055010012 16S rRNA interaction site [nucleotide binding]; other site 316055010013 streptomycin interaction site [chemical binding]; other site 316055010014 23S rRNA interaction site [nucleotide binding]; other site 316055010015 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 316055010016 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 316055010017 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055010018 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 316055010019 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 316055010020 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 316055010021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055010022 Walker A/P-loop; other site 316055010023 ATP binding site [chemical binding]; other site 316055010024 Q-loop/lid; other site 316055010025 ABC transporter signature motif; other site 316055010026 Walker B; other site 316055010027 D-loop; other site 316055010028 H-loop/switch region; other site 316055010029 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055010030 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 316055010031 Methyltransferase domain; Region: Methyltransf_11; pfam08241 316055010032 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 316055010033 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 316055010034 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 316055010035 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 316055010036 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 316055010037 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 316055010038 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 316055010039 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 316055010040 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 316055010041 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 316055010042 DNA binding site [nucleotide binding] 316055010043 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 316055010044 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 316055010045 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 316055010046 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 316055010047 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 316055010048 RPB11 interaction site [polypeptide binding]; other site 316055010049 RPB12 interaction site [polypeptide binding]; other site 316055010050 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 316055010051 RPB3 interaction site [polypeptide binding]; other site 316055010052 RPB1 interaction site [polypeptide binding]; other site 316055010053 RPB11 interaction site [polypeptide binding]; other site 316055010054 RPB10 interaction site [polypeptide binding]; other site 316055010055 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 316055010056 L11 interface [polypeptide binding]; other site 316055010057 putative EF-Tu interaction site [polypeptide binding]; other site 316055010058 putative EF-G interaction site [polypeptide binding]; other site 316055010059 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 316055010060 23S rRNA interface [nucleotide binding]; other site 316055010061 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 316055010062 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316055010063 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055010064 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055010065 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 316055010066 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 316055010067 catalytic loop [active] 316055010068 iron binding site [ion binding]; other site 316055010069 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316055010070 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 316055010071 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 316055010072 putative ligand binding site [chemical binding]; other site 316055010073 NAD binding site [chemical binding]; other site 316055010074 catalytic site [active] 316055010075 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 316055010076 mRNA/rRNA interface [nucleotide binding]; other site 316055010077 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 316055010078 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 316055010079 23S rRNA interface [nucleotide binding]; other site 316055010080 L7/L12 interface [polypeptide binding]; other site 316055010081 putative thiostrepton binding site; other site 316055010082 L25 interface [polypeptide binding]; other site 316055010083 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 316055010084 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 316055010085 putative homodimer interface [polypeptide binding]; other site 316055010086 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 316055010087 heterodimer interface [polypeptide binding]; other site 316055010088 homodimer interface [polypeptide binding]; other site 316055010089 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 316055010090 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 316055010091 Staphylococcal nuclease homologues; Region: SNc; smart00318 316055010092 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 316055010093 Catalytic site; other site 316055010094 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055010095 dimerization interface [polypeptide binding]; other site 316055010096 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055010097 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055010098 dimer interface [polypeptide binding]; other site 316055010099 putative CheW interface [polypeptide binding]; other site 316055010100 elongation factor Tu; Reviewed; Region: PRK00049 316055010101 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 316055010102 G1 box; other site 316055010103 GEF interaction site [polypeptide binding]; other site 316055010104 GTP/Mg2+ binding site [chemical binding]; other site 316055010105 Switch I region; other site 316055010106 G2 box; other site 316055010107 G3 box; other site 316055010108 Switch II region; other site 316055010109 G4 box; other site 316055010110 G5 box; other site 316055010111 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 316055010112 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 316055010113 Antibiotic Binding Site [chemical binding]; other site 316055010114 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055010115 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055010116 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 316055010117 classical (c) SDRs; Region: SDR_c; cd05233 316055010118 NAD(P) binding site [chemical binding]; other site 316055010119 active site 316055010120 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 316055010121 catalytic core [active] 316055010122 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055010123 classical (c) SDRs; Region: SDR_c; cd05233 316055010124 NAD(P) binding site [chemical binding]; other site 316055010125 active site 316055010126 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 316055010127 Phosphotransferase enzyme family; Region: APH; pfam01636 316055010128 putative active site [active] 316055010129 putative substrate binding site [chemical binding]; other site 316055010130 ATP binding site [chemical binding]; other site 316055010131 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055010132 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055010133 active site 316055010134 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055010135 Uncharacterized protein conserved in bacteria (DUF2087); Region: DUF2087; pfam09860 316055010136 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055010137 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055010138 TAP-like protein; Region: Abhydrolase_4; pfam08386 316055010139 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 316055010140 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 316055010141 dimer interface [polypeptide binding]; other site 316055010142 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055010143 catalytic residue [active] 316055010144 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 316055010145 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055010146 putative active site [active] 316055010147 heme pocket [chemical binding]; other site 316055010148 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 316055010149 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055010150 putative active site [active] 316055010151 heme pocket [chemical binding]; other site 316055010152 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 316055010153 putative active site [active] 316055010154 heme pocket [chemical binding]; other site 316055010155 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055010156 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 316055010157 ATP binding site [chemical binding]; other site 316055010158 Mg2+ binding site [ion binding]; other site 316055010159 G-X-G motif; other site 316055010160 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 316055010161 active site 316055010162 phosphorylation site [posttranslational modification] 316055010163 intermolecular recognition site; other site 316055010164 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 316055010165 Response regulator receiver domain; Region: Response_reg; pfam00072 316055010166 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 316055010167 active site 316055010168 phosphorylation site [posttranslational modification] 316055010169 intermolecular recognition site; other site 316055010170 dimerization interface [polypeptide binding]; other site 316055010171 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 316055010172 putative binding surface; other site 316055010173 active site 316055010174 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316055010175 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 316055010176 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 316055010177 ATP binding site [chemical binding]; other site 316055010178 Mg2+ binding site [ion binding]; other site 316055010179 G-X-G motif; other site 316055010180 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 316055010181 Response regulator receiver domain; Region: Response_reg; pfam00072 316055010182 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 316055010183 active site 316055010184 phosphorylation site [posttranslational modification] 316055010185 intermolecular recognition site; other site 316055010186 dimerization interface [polypeptide binding]; other site 316055010187 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316055010188 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 316055010189 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 316055010190 HEAT repeats; Region: HEAT_2; pfam13646 316055010191 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 316055010192 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 316055010193 active site 316055010194 phosphorylation site [posttranslational modification] 316055010195 intermolecular recognition site; other site 316055010196 dimerization interface [polypeptide binding]; other site 316055010197 CheB methylesterase; Region: CheB_methylest; pfam01339 316055010198 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 316055010199 CheW-like domain; Region: CheW; pfam01584 316055010200 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 316055010201 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055010202 putative CheW interface [polypeptide binding]; other site 316055010203 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 316055010204 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055010205 dimer interface [polypeptide binding]; other site 316055010206 putative CheW interface [polypeptide binding]; other site 316055010207 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 316055010208 Chemotaxis phosphatase CheX; Region: CheX; cl15816 316055010209 Chemotaxis phosphatase CheX; Region: CheX; cl15816 316055010210 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 316055010211 Predicted membrane protein [Function unknown]; Region: COG2261 316055010212 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055010213 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 316055010214 catalytic site [active] 316055010215 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 316055010216 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055010217 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 316055010218 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 316055010219 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 316055010220 dimanganese center [ion binding]; other site 316055010221 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 316055010222 metal binding site [ion binding]; metal-binding site 316055010223 dimerization interface [polypeptide binding]; other site 316055010224 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055010225 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 316055010226 putative catalytic site [active] 316055010227 putative phosphate binding site [ion binding]; other site 316055010228 active site 316055010229 metal binding site A [ion binding]; metal-binding site 316055010230 DNA binding site [nucleotide binding] 316055010231 putative AP binding site [nucleotide binding]; other site 316055010232 putative metal binding site B [ion binding]; other site 316055010233 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 316055010234 short chain dehydrogenase; Provisional; Region: PRK06701 316055010235 NAD binding site [chemical binding]; other site 316055010236 metal binding site [ion binding]; metal-binding site 316055010237 active site 316055010238 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 316055010239 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316055010240 NAD binding site [chemical binding]; other site 316055010241 catalytic Zn binding site [ion binding]; other site 316055010242 structural Zn binding site [ion binding]; other site 316055010243 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 316055010244 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 316055010245 putative molybdopterin cofactor binding site [chemical binding]; other site 316055010246 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 316055010247 putative molybdopterin cofactor binding site; other site 316055010248 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 316055010249 Putative glucoamylase; Region: Glycoamylase; pfam10091 316055010250 Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_2_like; cd11753 316055010251 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 316055010252 First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_1_like; cd11756 316055010253 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 316055010254 HWE histidine kinase; Region: HWE_HK; smart00911 316055010255 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055010256 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 316055010257 ligand binding site [chemical binding]; other site 316055010258 flexible hinge region; other site 316055010259 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 316055010260 non-specific DNA interactions [nucleotide binding]; other site 316055010261 DNA binding site [nucleotide binding] 316055010262 sequence specific DNA binding site [nucleotide binding]; other site 316055010263 putative cAMP binding site [chemical binding]; other site 316055010264 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 316055010265 Sodium Bile acid symporter family; Region: SBF; cl17470 316055010266 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 316055010267 ArsC family; Region: ArsC; pfam03960 316055010268 catalytic residues [active] 316055010269 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 316055010270 Low molecular weight phosphatase family; Region: LMWPc; cl00105 316055010271 active site 316055010272 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 316055010273 putative Zn2+ binding site [ion binding]; other site 316055010274 putative DNA binding site [nucleotide binding]; other site 316055010275 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 316055010276 Predicted permeases [General function prediction only]; Region: COG0701 316055010277 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 316055010278 putative Zn2+ binding site [ion binding]; other site 316055010279 putative DNA binding site [nucleotide binding]; other site 316055010280 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 316055010281 dimerization interface [polypeptide binding]; other site 316055010282 metal binding site [ion binding]; metal-binding site 316055010283 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 316055010284 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055010285 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055010286 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 316055010287 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 316055010288 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 316055010289 4Fe-4S binding domain; Region: Fer4_5; pfam12801 316055010290 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 316055010291 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 316055010292 Fe2+ transport protein; Region: Iron_transport; pfam10634 316055010293 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055010294 short chain dehydrogenase; Provisional; Region: PRK07832 316055010295 NAD(P) binding site [chemical binding]; other site 316055010296 active site 316055010297 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055010298 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055010299 putative magnesium chelatase accessory protein; Region: bchO_mg_che_rel; TIGR03056 316055010300 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055010301 Cupin domain; Region: Cupin_2; pfam07883 316055010302 Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; Region: RLP_RrRLP; cd08210 316055010303 dimer interface [polypeptide binding]; other site 316055010304 active site 316055010305 catalytic residue [active] 316055010306 metal binding site [ion binding]; metal-binding site 316055010307 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 316055010308 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 316055010309 G1 box; other site 316055010310 GTP/Mg2+ binding site [chemical binding]; other site 316055010311 Switch I region; other site 316055010312 G2 box; other site 316055010313 G3 box; other site 316055010314 Switch II region; other site 316055010315 G4 box; other site 316055010316 G5 box; other site 316055010317 Nucleoside recognition; Region: Gate; pfam07670 316055010318 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 316055010319 Nucleoside recognition; Region: Gate; pfam07670 316055010320 FeoA domain; Region: FeoA; pfam04023 316055010321 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 316055010322 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 316055010323 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 316055010324 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055010325 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 316055010326 putative NAD(P) binding site [chemical binding]; other site 316055010327 active site 316055010328 putative substrate binding site [chemical binding]; other site 316055010329 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 316055010330 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055010331 dimer interface [polypeptide binding]; other site 316055010332 conserved gate region; other site 316055010333 putative PBP binding loops; other site 316055010334 ABC-ATPase subunit interface; other site 316055010335 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055010336 dimer interface [polypeptide binding]; other site 316055010337 conserved gate region; other site 316055010338 putative PBP binding loops; other site 316055010339 ABC-ATPase subunit interface; other site 316055010340 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 316055010341 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 316055010342 Walker A/P-loop; other site 316055010343 ATP binding site [chemical binding]; other site 316055010344 Q-loop/lid; other site 316055010345 ABC transporter signature motif; other site 316055010346 Walker B; other site 316055010347 D-loop; other site 316055010348 H-loop/switch region; other site 316055010349 TOBE domain; Region: TOBE_2; pfam08402 316055010350 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 316055010351 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 316055010352 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055010353 NAD(P) binding site [chemical binding]; other site 316055010354 active site 316055010355 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055010356 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055010357 NAD(P) binding site [chemical binding]; other site 316055010358 active site 316055010359 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 316055010360 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 316055010361 putative catalytic cysteine [active] 316055010362 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 316055010363 putative active site [active] 316055010364 metal binding site [ion binding]; metal-binding site 316055010365 Phasin protein; Region: Phasin_2; cl11491 316055010366 HAMP domain; Region: HAMP; pfam00672 316055010367 dimerization interface [polypeptide binding]; other site 316055010368 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055010369 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055010370 metal binding site [ion binding]; metal-binding site 316055010371 active site 316055010372 I-site; other site 316055010373 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 316055010374 DDE superfamily endonuclease; Region: DDE_3; pfam13358 316055010375 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 316055010376 Winged helix-turn helix; Region: HTH_29; pfam13551 316055010377 Helix-turn-helix domain; Region: HTH_28; pfam13518 316055010378 Homeodomain-like domain; Region: HTH_32; pfam13565 316055010379 Rad4 beta-hairpin domain 3; Region: BHD_3; cl11064 316055010380 Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Region: GIY-YIG_SLX1_like; cd10449 316055010381 GIY-YIG motif/motif A; other site 316055010382 putative active site [active] 316055010383 putative metal binding site [ion binding]; other site 316055010384 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 316055010385 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 316055010386 catalytic residues [active] 316055010387 dimer interface [polypeptide binding]; other site 316055010388 amidase; Provisional; Region: PRK07487 316055010389 Amidase; Region: Amidase; cl11426 316055010390 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 316055010391 TAP-like protein; Region: Abhydrolase_4; pfam08386 316055010392 DsrE/DsrF-like family; Region: DrsE; cl00672 316055010393 bifunctional transaldolase/phosoglucose isomerase; Validated; Region: PRK09533 316055010394 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 316055010395 putative active site [active] 316055010396 catalytic residue [active] 316055010397 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 316055010398 SIS_TAL_PGI: Transaldolase (TAL)/ Phosphoglucose isomerase (PGI). This group represents the SIS (Sugar ISomerase) PGI domain, of a multifunctional protein (TAL-PGI ) having both TAL and PGI activities. TAL_PGI contains an N-terminal TAL domain and a...; Region: SIS_TAL_PGI; cd05798 316055010399 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 316055010400 Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG1023 316055010401 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 316055010402 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 316055010403 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 316055010404 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 316055010405 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 316055010406 putative active site [active] 316055010407 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 316055010408 AAA domain; Region: AAA_33; pfam13671 316055010409 ATP-binding site [chemical binding]; other site 316055010410 Gluconate-6-phosphate binding site [chemical binding]; other site 316055010411 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 316055010412 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 316055010413 active site 316055010414 motif I; other site 316055010415 motif II; other site 316055010416 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 316055010417 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 316055010418 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 316055010419 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 316055010420 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 316055010421 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 316055010422 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 316055010423 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 316055010424 active site 316055010425 homodimer interface [polypeptide binding]; other site 316055010426 catalytic site [active] 316055010427 acceptor binding site [chemical binding]; other site 316055010428 trehalose synthase; Region: treS_nterm; TIGR02456 316055010429 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 316055010430 active site 316055010431 catalytic site [active] 316055010432 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 316055010433 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 316055010434 glycogen branching enzyme; Provisional; Region: PRK05402 316055010435 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 316055010436 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 316055010437 active site 316055010438 catalytic site [active] 316055010439 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 316055010440 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 316055010441 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 316055010442 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 316055010443 active site 316055010444 catalytic site [active] 316055010445 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 316055010446 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 316055010447 MOFRL family; Region: MOFRL; pfam05161 316055010448 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 316055010449 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 316055010450 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 316055010451 active site 316055010452 catalytic site [active] 316055010453 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 316055010454 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 316055010455 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 316055010456 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 316055010457 active site 316055010458 DNA binding site [nucleotide binding] 316055010459 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 316055010460 DNA binding site [nucleotide binding] 316055010461 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 316055010462 nucleotide binding site [chemical binding]; other site 316055010463 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 316055010464 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 316055010465 putative DNA binding site [nucleotide binding]; other site 316055010466 putative homodimer interface [polypeptide binding]; other site 316055010467 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 316055010468 CPxP motif; other site 316055010469 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 316055010470 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 316055010471 GTP binding site; other site 316055010472 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 316055010473 UreF; Region: UreF; pfam01730 316055010474 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 316055010475 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 316055010476 dimer interface [polypeptide binding]; other site 316055010477 catalytic residues [active] 316055010478 Uncharacterized conserved protein [Function unknown]; Region: COG1359 316055010479 urease subunit alpha; Reviewed; Region: ureC; PRK13207 316055010480 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 316055010481 subunit interactions [polypeptide binding]; other site 316055010482 active site 316055010483 flap region; other site 316055010484 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 316055010485 HD domain; Region: HD_4; pfam13328 316055010486 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 316055010487 gamma-beta subunit interface [polypeptide binding]; other site 316055010488 alpha-beta subunit interface [polypeptide binding]; other site 316055010489 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 316055010490 alpha-gamma subunit interface [polypeptide binding]; other site 316055010491 beta-gamma subunit interface [polypeptide binding]; other site 316055010492 UreD urease accessory protein; Region: UreD; pfam01774 316055010493 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 316055010494 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055010495 Walker A/P-loop; other site 316055010496 ATP binding site [chemical binding]; other site 316055010497 Q-loop/lid; other site 316055010498 ABC transporter signature motif; other site 316055010499 Walker B; other site 316055010500 D-loop; other site 316055010501 H-loop/switch region; other site 316055010502 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 316055010503 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055010504 Walker A/P-loop; other site 316055010505 ATP binding site [chemical binding]; other site 316055010506 Q-loop/lid; other site 316055010507 ABC transporter signature motif; other site 316055010508 Walker B; other site 316055010509 D-loop; other site 316055010510 H-loop/switch region; other site 316055010511 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055010512 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 316055010513 TM-ABC transporter signature motif; other site 316055010514 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 316055010515 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055010516 TM-ABC transporter signature motif; other site 316055010517 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010518 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 316055010519 putative ligand binding site [chemical binding]; other site 316055010520 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 316055010521 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 316055010522 ATP binding site [chemical binding]; other site 316055010523 Mg++ binding site [ion binding]; other site 316055010524 motif III; other site 316055010525 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 316055010526 nucleotide binding region [chemical binding]; other site 316055010527 ATP-binding site [chemical binding]; other site 316055010528 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 316055010529 rRNA binding site [nucleotide binding]; other site 316055010530 predicted 30S ribosome binding site; other site 316055010531 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055010532 DNA-binding site [nucleotide binding]; DNA binding site 316055010533 RNA-binding motif; other site 316055010534 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 316055010535 TadE-like protein; Region: TadE; pfam07811 316055010536 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 316055010537 TadE-like protein; Region: TadE; pfam07811 316055010538 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 316055010539 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 316055010540 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 316055010541 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 316055010542 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 316055010543 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 316055010544 Type IV pili component [Cell motility and secretion]; Region: COG5461 316055010545 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 316055010546 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 contains...; Region: CpaE_like; cd03111 316055010547 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 316055010548 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 316055010549 ATP binding site [chemical binding]; other site 316055010550 Walker A motif; other site 316055010551 hexamer interface [polypeptide binding]; other site 316055010552 Walker B motif; other site 316055010553 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 316055010554 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 316055010555 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 316055010556 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 316055010557 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 316055010558 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 316055010559 binding surface 316055010560 TPR motif; other site 316055010561 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 316055010562 TPR motif; other site 316055010563 binding surface 316055010564 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 316055010565 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 316055010566 interface (dimer of trimers) [polypeptide binding]; other site 316055010567 Substrate-binding/catalytic site; other site 316055010568 Zn-binding sites [ion binding]; other site 316055010569 Bacterial SH3 domain; Region: SH3_4; pfam06347 316055010570 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 316055010571 NlpC/P60 family; Region: NLPC_P60; cl17555 316055010572 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 316055010573 dimer interface [polypeptide binding]; other site 316055010574 active site 316055010575 ADP-ribose binding site [chemical binding]; other site 316055010576 nudix motif; other site 316055010577 metal binding site [ion binding]; metal-binding site 316055010578 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 316055010579 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 316055010580 Walker A/P-loop; other site 316055010581 ATP binding site [chemical binding]; other site 316055010582 Q-loop/lid; other site 316055010583 ABC transporter signature motif; other site 316055010584 Walker B; other site 316055010585 D-loop; other site 316055010586 H-loop/switch region; other site 316055010587 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316055010588 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 316055010589 Walker A/P-loop; other site 316055010590 ATP binding site [chemical binding]; other site 316055010591 Q-loop/lid; other site 316055010592 ABC transporter signature motif; other site 316055010593 Walker B; other site 316055010594 D-loop; other site 316055010595 H-loop/switch region; other site 316055010596 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316055010597 PIN domain; Region: PIN; pfam01850 316055010598 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 316055010599 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055010600 dimer interface [polypeptide binding]; other site 316055010601 conserved gate region; other site 316055010602 ABC-ATPase subunit interface; other site 316055010603 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 316055010604 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055010605 dimer interface [polypeptide binding]; other site 316055010606 conserved gate region; other site 316055010607 putative PBP binding loops; other site 316055010608 ABC-ATPase subunit interface; other site 316055010609 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 316055010610 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 316055010611 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 316055010612 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 316055010613 Cytochrome c2 [Energy production and conversion]; Region: COG3474 316055010614 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 316055010615 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 316055010616 Ligand binding site; other site 316055010617 oligomer interface; other site 316055010618 prephenate dehydratase; Provisional; Region: PRK11899 316055010619 Prephenate dehydratase; Region: PDT; pfam00800 316055010620 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 316055010621 putative L-Phe binding site [chemical binding]; other site 316055010622 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 316055010623 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 316055010624 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 316055010625 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 316055010626 FAD binding site [chemical binding]; other site 316055010627 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 316055010628 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 316055010629 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 316055010630 substrate binding pocket [chemical binding]; other site 316055010631 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 316055010632 B12 binding site [chemical binding]; other site 316055010633 cobalt ligand [ion binding]; other site 316055010634 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 316055010635 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 316055010636 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 316055010637 N- and C-terminal domain interface [polypeptide binding]; other site 316055010638 active site 316055010639 MgATP binding site [chemical binding]; other site 316055010640 catalytic site [active] 316055010641 metal binding site [ion binding]; metal-binding site 316055010642 glycerol binding site [chemical binding]; other site 316055010643 homotetramer interface [polypeptide binding]; other site 316055010644 homodimer interface [polypeptide binding]; other site 316055010645 FBP binding site [chemical binding]; other site 316055010646 protein IIAGlc interface [polypeptide binding]; other site 316055010647 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 316055010648 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 316055010649 active site 316055010650 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 316055010651 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055010652 active site 316055010653 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055010654 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055010655 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055010656 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 316055010657 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 316055010658 dimer interface [polypeptide binding]; other site 316055010659 active site 316055010660 dicarboxylate--CoA ligase PimA; Region: pimA; TIGR03205 316055010661 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 316055010662 acyl-activating enzyme (AAE) consensus motif; other site 316055010663 putative AMP binding site [chemical binding]; other site 316055010664 putative active site [active] 316055010665 putative CoA binding site [chemical binding]; other site 316055010666 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 316055010667 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 316055010668 substrate binding site [chemical binding]; other site 316055010669 oxyanion hole (OAH) forming residues; other site 316055010670 trimer interface [polypeptide binding]; other site 316055010671 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 316055010672 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316055010673 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316055010674 Transcriptional regulator [Transcription]; Region: IclR; COG1414 316055010675 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 316055010676 Bacterial transcriptional regulator; Region: IclR; pfam01614 316055010677 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055010678 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055010679 Walker A/P-loop; other site 316055010680 ATP binding site [chemical binding]; other site 316055010681 Q-loop/lid; other site 316055010682 ABC transporter signature motif; other site 316055010683 Walker B; other site 316055010684 D-loop; other site 316055010685 H-loop/switch region; other site 316055010686 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055010687 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055010688 Walker A/P-loop; other site 316055010689 ATP binding site [chemical binding]; other site 316055010690 Q-loop/lid; other site 316055010691 ABC transporter signature motif; other site 316055010692 Walker B; other site 316055010693 D-loop; other site 316055010694 H-loop/switch region; other site 316055010695 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055010696 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 316055010697 TM-ABC transporter signature motif; other site 316055010698 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055010699 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 316055010700 TM-ABC transporter signature motif; other site 316055010701 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055010702 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010703 putative ligand binding site [chemical binding]; other site 316055010704 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055010705 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010706 putative ligand binding site [chemical binding]; other site 316055010707 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055010708 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010709 putative ligand binding site [chemical binding]; other site 316055010710 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 316055010711 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010712 putative ligand binding site [chemical binding]; other site 316055010713 Protein of unknown function (DUF3124); Region: DUF3124; pfam11322 316055010714 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 316055010715 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 316055010716 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 316055010717 TrkA-N domain; Region: TrkA_N; pfam02254 316055010718 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055010719 dimerization interface [polypeptide binding]; other site 316055010720 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055010721 dimer interface [polypeptide binding]; other site 316055010722 putative CheW interface [polypeptide binding]; other site 316055010723 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 316055010724 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055010725 P-loop; other site 316055010726 Magnesium ion binding site [ion binding]; other site 316055010727 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 316055010728 MarR family; Region: MarR; pfam01047 316055010729 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055010730 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 316055010731 TM-ABC transporter signature motif; other site 316055010732 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055010733 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 316055010734 TM-ABC transporter signature motif; other site 316055010735 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055010736 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055010737 Walker A/P-loop; other site 316055010738 ATP binding site [chemical binding]; other site 316055010739 Q-loop/lid; other site 316055010740 ABC transporter signature motif; other site 316055010741 Walker B; other site 316055010742 D-loop; other site 316055010743 H-loop/switch region; other site 316055010744 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055010745 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055010746 Walker A/P-loop; other site 316055010747 ATP binding site [chemical binding]; other site 316055010748 Q-loop/lid; other site 316055010749 ABC transporter signature motif; other site 316055010750 Walker B; other site 316055010751 D-loop; other site 316055010752 H-loop/switch region; other site 316055010753 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 316055010754 PAS domain; Region: PAS_9; pfam13426 316055010755 putative active site [active] 316055010756 heme pocket [chemical binding]; other site 316055010757 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055010758 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055010759 metal binding site [ion binding]; metal-binding site 316055010760 active site 316055010761 I-site; other site 316055010762 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055010763 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 316055010764 putative ligand binding site [chemical binding]; other site 316055010765 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055010766 active site 316055010767 feruloyl-CoA synthase; Reviewed; Region: PRK08180 316055010768 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 316055010769 acyl-activating enzyme (AAE) consensus motif; other site 316055010770 putative AMP binding site [chemical binding]; other site 316055010771 putative active site [active] 316055010772 putative CoA binding site [chemical binding]; other site 316055010773 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 316055010774 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 316055010775 substrate binding site [chemical binding]; other site 316055010776 oxyanion hole (OAH) forming residues; other site 316055010777 trimer interface [polypeptide binding]; other site 316055010778 hypothetical protein; Provisional; Region: PRK00872 316055010779 DctM-like transporters; Region: DctM; pfam06808 316055010780 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 316055010781 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 316055010782 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 316055010783 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 316055010784 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 316055010785 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055010786 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055010787 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055010788 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055010789 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055010790 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055010791 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 316055010792 putative effector binding pocket; other site 316055010793 putative dimerization interface [polypeptide binding]; other site 316055010794 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 316055010795 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 316055010796 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 316055010797 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 316055010798 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 316055010799 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 316055010800 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055010801 ligand binding site [chemical binding]; other site 316055010802 flexible hinge region; other site 316055010803 enoyl-CoA hydratase; Provisional; Region: PRK06127 316055010804 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 316055010805 substrate binding site [chemical binding]; other site 316055010806 oxyanion hole (OAH) forming residues; other site 316055010807 trimer interface [polypeptide binding]; other site 316055010808 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 source...; Region: Nitroreductase; cd02136 316055010809 putative FMN binding site [chemical binding]; other site 316055010810 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055010811 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 316055010812 FAD binding site [chemical binding]; other site 316055010813 substrate binding site [chemical binding]; other site 316055010814 catalytic base [active] 316055010815 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055010816 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055010817 active site 316055010818 acyl-CoA synthetase; Provisional; Region: PRK12582 316055010819 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 316055010820 acyl-activating enzyme (AAE) consensus motif; other site 316055010821 putative AMP binding site [chemical binding]; other site 316055010822 putative active site [active] 316055010823 putative CoA binding site [chemical binding]; other site 316055010824 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 316055010825 NAD binding site [chemical binding]; other site 316055010826 homodimer interface [polypeptide binding]; other site 316055010827 homotetramer interface [polypeptide binding]; other site 316055010828 active site 316055010829 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055010830 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055010831 acetyl-CoA acetyltransferase; Provisional; Region: PRK06504 316055010832 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 316055010833 dimer interface [polypeptide binding]; other site 316055010834 active site 316055010835 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055010836 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 316055010837 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055010838 acyl-activating enzyme (AAE) consensus motif; other site 316055010839 acyl-activating enzyme (AAE) consensus motif; other site 316055010840 putative AMP binding site [chemical binding]; other site 316055010841 putative active site [active] 316055010842 putative CoA binding site [chemical binding]; other site 316055010843 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316055010844 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 316055010845 catalytic residues [active] 316055010846 catalytic nucleophile [active] 316055010847 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 316055010848 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 316055010849 active site 316055010850 catalytic triad [active] 316055010851 oxyanion hole [active] 316055010852 Autotransporter beta-domain; Region: Autotransporter; pfam03797 316055010853 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055010854 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 316055010855 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 316055010856 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 316055010857 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055010858 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 316055010859 dimerization interface [polypeptide binding]; other site 316055010860 substrate binding pocket [chemical binding]; other site 316055010861 Competence-damaged protein; Region: CinA; pfam02464 316055010862 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 316055010863 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055010864 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055010865 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 316055010866 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 316055010867 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 316055010868 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 316055010869 putative substrate translocation pore; other site 316055010870 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055010871 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 316055010872 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_3; cd13148 316055010873 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 316055010874 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 316055010875 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 316055010876 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 316055010877 active site pocket [active] 316055010878 putative dimer interface [polypeptide binding]; other site 316055010879 putative cataytic base [active] 316055010880 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 316055010881 IHF dimer interface [polypeptide binding]; other site 316055010882 IHF - DNA interface [nucleotide binding]; other site 316055010883 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 316055010884 catalytic core [active] 316055010885 cobalamin synthase; Reviewed; Region: cobS; PRK00235 316055010886 HerA helicase [Replication, recombination, and repair]; Region: COG0433 316055010887 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055010888 Walker A motif; other site 316055010889 ATP binding site [chemical binding]; other site 316055010890 Walker B motif; other site 316055010891 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055010892 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055010893 Walker A/P-loop; other site 316055010894 ATP binding site [chemical binding]; other site 316055010895 Q-loop/lid; other site 316055010896 ABC transporter signature motif; other site 316055010897 Walker B; other site 316055010898 D-loop; other site 316055010899 H-loop/switch region; other site 316055010900 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055010901 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055010902 Walker A/P-loop; other site 316055010903 ATP binding site [chemical binding]; other site 316055010904 Q-loop/lid; other site 316055010905 ABC transporter signature motif; other site 316055010906 Walker B; other site 316055010907 D-loop; other site 316055010908 H-loop/switch region; other site 316055010909 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055010910 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 316055010911 TM-ABC transporter signature motif; other site 316055010912 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 316055010913 TM-ABC transporter signature motif; other site 316055010914 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055010915 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 316055010916 putative ligand binding site [chemical binding]; other site 316055010917 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 basis...; Region: HIT_like; cl00228 316055010918 nucleotide binding site/active site [active] 316055010919 HIT family signature motif; other site 316055010920 catalytic residue [active] 316055010921 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 316055010922 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 316055010923 N-terminal plug; other site 316055010924 ligand-binding site [chemical binding]; other site 316055010925 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 316055010926 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055010927 Walker A/P-loop; other site 316055010928 ATP binding site [chemical binding]; other site 316055010929 Q-loop/lid; other site 316055010930 ABC transporter signature motif; other site 316055010931 Walker B; other site 316055010932 D-loop; other site 316055010933 H-loop/switch region; other site 316055010934 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 316055010935 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055010936 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 316055010937 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 316055010938 catalytic loop [active] 316055010939 iron binding site [ion binding]; other site 316055010940 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 316055010941 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 316055010942 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 316055010943 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 316055010944 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 316055010945 glutamate synthase (NADPH), homotetrameric; Region: gltA; TIGR01316 316055010946 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055010947 propionate/acetate kinase; Provisional; Region: PRK12379 316055010948 Acetokinase family; Region: Acetate_kinase; cl17229 316055010949 phosphate acetyltransferase; Reviewed; Region: PRK05632 316055010950 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055010951 DRTGG domain; Region: DRTGG; pfam07085 316055010952 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 316055010953 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; pfam09678 316055010954 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 316055010955 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 316055010956 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 316055010957 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 316055010958 D-pathway; other site 316055010959 Putative ubiquinol binding site [chemical binding]; other site 316055010960 Low-spin heme (heme b) binding site [chemical binding]; other site 316055010961 Putative water exit pathway; other site 316055010962 Binuclear center (heme o3/CuB) [ion binding]; other site 316055010963 K-pathway; other site 316055010964 Putative proton exit pathway; other site 316055010965 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 316055010966 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 316055010967 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 316055010968 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 316055010969 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055010970 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055010971 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK08600 316055010972 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 316055010973 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 316055010974 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 316055010975 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 316055010976 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 316055010977 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316055010978 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 316055010979 active site 316055010980 motif I; other site 316055010981 motif II; other site 316055010982 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 316055010983 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055010984 Walker A motif; other site 316055010985 ATP binding site [chemical binding]; other site 316055010986 Walker B motif; other site 316055010987 arginine finger; other site 316055010988 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055010989 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 316055010990 putative active site pocket [active] 316055010991 dimerization interface [polypeptide binding]; other site 316055010992 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; cl15777 316055010993 putative catalytic residue [active] 316055010994 Iron only nitrogenase protein AnfO (AnfO_nitrog); Region: AnfO_nitrog; pfam09582 316055010995 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 316055010996 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 316055010997 Vanadium/alternative nitrogenase delta subunit; Region: AnfG_VnfG; pfam03139 316055010998 nitrogenase iron-iron protein, alpha chain; Region: ANFD; TIGR01861 316055010999 Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of, the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase...; Region: Nitrogenase_VFe_alpha; cd01977 316055011000 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family; Region: Fer4_NifH; pfam00142 316055011001 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 316055011002 Nucleotide-binding sites [chemical binding]; other site 316055011003 Switch I region of nucleotide binding site; other site 316055011004 Fe4S4 binding sites [ion binding]; other site 316055011005 Switch II region of nucleotide binding site; other site 316055011006 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 316055011007 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 316055011008 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055011009 Walker A motif; other site 316055011010 ATP binding site [chemical binding]; other site 316055011011 Walker B motif; other site 316055011012 arginine finger; other site 316055011013 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055011014 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 316055011015 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 316055011016 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316055011017 DNA-binding site [nucleotide binding]; DNA binding site 316055011018 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 316055011019 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055011020 homodimer interface [polypeptide binding]; other site 316055011021 catalytic residue [active] 316055011022 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 316055011023 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 316055011024 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055011025 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055011026 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055011027 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055011028 Walker A/P-loop; other site 316055011029 ATP binding site [chemical binding]; other site 316055011030 Q-loop/lid; other site 316055011031 ABC transporter signature motif; other site 316055011032 Walker B; other site 316055011033 D-loop; other site 316055011034 H-loop/switch region; other site 316055011035 AAK_UMPK-MosAB: This CD includes the alpha and beta subunits of the Mo storage protein (MosA and MosB) which are related to uridine monophosphate kinase (UMPK) enzymes that catalyze the phosphorylation of UMP by ATP, yielding UDP, and playing a key role...; Region: AAK_UMPK-MosAB; cd04255 316055011036 putative nucleotide binding site [chemical binding]; other site 316055011037 putative substrate binding site [chemical binding]; other site 316055011038 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 316055011039 nucleotide binding site [chemical binding]; other site 316055011040 substrate binding site [chemical binding]; other site 316055011041 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 316055011042 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 316055011043 Predicted membrane protein [Function unknown]; Region: COG3212 316055011044 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 316055011045 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 316055011046 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 316055011047 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 316055011048 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 316055011049 FAD binding pocket [chemical binding]; other site 316055011050 FAD binding motif [chemical binding]; other site 316055011051 phosphate binding motif [ion binding]; other site 316055011052 beta-alpha-beta structure motif; other site 316055011053 NAD binding pocket [chemical binding]; other site 316055011054 hypothetical protein; Provisional; Region: PRK10428 316055011055 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 316055011056 putative beta-lysine N-acetyltransferase; Region: GNAT_ablB; TIGR03827 316055011057 Acyl-CoA reductase LuxC; Region: ALDH_Acyl-CoA-Red_LuxC; cd07080 316055011058 Acyl-CoA reductase (LuxC); Region: LuxC; pfam05893 316055011059 putative catalytic cysteine [active] 316055011060 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 316055011061 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055011062 acyl-activating enzyme (AAE) consensus motif; other site 316055011063 AMP binding site [chemical binding]; other site 316055011064 active site 316055011065 CoA binding site [chemical binding]; other site 316055011066 Acyl-protein synthetase, LuxE; Region: LuxE; pfam04443 316055011067 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 316055011068 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055011069 acyl-activating enzyme (AAE) consensus motif; other site 316055011070 AMP binding site [chemical binding]; other site 316055011071 active site 316055011072 CoA binding site [chemical binding]; other site 316055011073 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 316055011074 H+ Antiporter protein; Region: 2A0121; TIGR00900 316055011075 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 316055011076 anti sigma factor interaction site; other site 316055011077 regulatory phosphorylation site [posttranslational modification]; other site 316055011078 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 316055011079 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 316055011080 ATP binding site [chemical binding]; other site 316055011081 Mg2+ binding site [ion binding]; other site 316055011082 G-X-G motif; other site 316055011083 NMT1/THI5 like; Region: NMT1; pfam09084 316055011084 Cache domain; Region: Cache_1; pfam02743 316055011085 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055011086 dimerization interface [polypeptide binding]; other site 316055011087 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 316055011088 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 316055011089 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 316055011090 NAD(P) binding site [chemical binding]; other site 316055011091 catalytic residues [active] 316055011092 choline dehydrogenase; Validated; Region: PRK02106 316055011093 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 316055011094 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 316055011095 short chain dehydrogenase; Provisional; Region: PRK06949 316055011096 classical (c) SDRs; Region: SDR_c; cd05233 316055011097 NAD(P) binding site [chemical binding]; other site 316055011098 active site 316055011099 Colicin V production protein; Region: Colicin_V; pfam02674 316055011100 short chain dehydrogenase; Provisional; Region: PRK08339 316055011101 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 316055011102 putative NAD(P) binding site [chemical binding]; other site 316055011103 putative active site [active] 316055011104 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 316055011105 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 316055011106 active site 316055011107 phosphorylation site [posttranslational modification] 316055011108 intermolecular recognition site; other site 316055011109 dimerization interface [polypeptide binding]; other site 316055011110 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055011111 DNA binding residues [nucleotide binding] 316055011112 dimerization interface [polypeptide binding]; other site 316055011113 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 316055011114 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055011115 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055011116 dimer interface [polypeptide binding]; other site 316055011117 phosphorylation site [posttranslational modification] 316055011118 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 316055011119 ATP binding site [chemical binding]; other site 316055011120 Mg2+ binding site [ion binding]; other site 316055011121 G-X-G motif; other site 316055011122 Response regulator receiver domain; Region: Response_reg; pfam00072 316055011123 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 316055011124 active site 316055011125 phosphorylation site [posttranslational modification] 316055011126 intermolecular recognition site; other site 316055011127 dimerization interface [polypeptide binding]; other site 316055011128 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 316055011129 putative binding surface; other site 316055011130 active site 316055011131 Response regulator receiver domain; Region: Response_reg; pfam00072 316055011132 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 316055011133 active site 316055011134 phosphorylation site [posttranslational modification] 316055011135 intermolecular recognition site; other site 316055011136 dimerization interface [polypeptide binding]; other site 316055011137 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 316055011138 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316055011139 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 316055011140 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 316055011141 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 316055011142 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 316055011143 putative binding surface; other site 316055011144 active site 316055011145 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 316055011146 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316055011147 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 316055011148 ATP binding site [chemical binding]; other site 316055011149 Mg2+ binding site [ion binding]; other site 316055011150 G-X-G motif; other site 316055011151 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 316055011152 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055011153 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 316055011154 active site 316055011155 phosphorylation site [posttranslational modification] 316055011156 intermolecular recognition site; other site 316055011157 dimerization interface [polypeptide binding]; other site 316055011158 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055011159 dimerization interface [polypeptide binding]; other site 316055011160 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011161 dimer interface [polypeptide binding]; other site 316055011162 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055011163 putative CheW interface [polypeptide binding]; other site 316055011164 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055011165 dimerization interface [polypeptide binding]; other site 316055011166 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011167 dimer interface [polypeptide binding]; other site 316055011168 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055011169 putative CheW interface [polypeptide binding]; other site 316055011170 Response regulator receiver domain; Region: Response_reg; pfam00072 316055011171 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 316055011172 active site 316055011173 phosphorylation site [posttranslational modification] 316055011174 intermolecular recognition site; other site 316055011175 dimerization interface [polypeptide binding]; other site 316055011176 BON domain; Region: BON; pfam04972 316055011177 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 316055011178 BON domain; Region: BON; pfam04972 316055011179 BON domain; Region: BON; pfam04972 316055011180 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 316055011181 Catalytic domain of Protein Kinases; Region: PKc; cd00180 316055011182 active site 316055011183 ATP binding site [chemical binding]; other site 316055011184 substrate binding site [chemical binding]; other site 316055011185 activation loop (A-loop); other site 316055011186 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 316055011187 Ligand Binding Site [chemical binding]; other site 316055011188 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316055011189 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 316055011190 active site 316055011191 metal binding site [ion binding]; metal-binding site 316055011192 silicon transporter; Region: sit; TIGR00811 316055011193 magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; Region: BchE; TIGR02026 316055011194 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 316055011195 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 316055011196 FeS/SAM binding site; other site 316055011197 V4R domain; Region: V4R; cl15268 316055011198 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 316055011199 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 316055011200 FeS/SAM binding site; other site 316055011201 HemN C-terminal domain; Region: HemN_C; pfam06969 316055011202 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 316055011203 putative homodimer interface [polypeptide binding]; other site 316055011204 putative homotetramer interface [polypeptide binding]; other site 316055011205 putative allosteric switch controlling residues; other site 316055011206 putative metal binding site [ion binding]; other site 316055011207 putative homodimer-homodimer interface [polypeptide binding]; other site 316055011208 YHS domain; Region: YHS; pfam04945 316055011209 YHS domain; Region: YHS; pfam04945 316055011210 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 316055011211 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316055011212 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 316055011213 motif II; other site 316055011214 Hemerythrin-like domain; Region: Hr-like; cd12108 316055011215 Fe binding site [ion binding]; other site 316055011216 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 316055011217 active site 316055011218 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055011219 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055011220 metal binding site [ion binding]; metal-binding site 316055011221 active site 316055011222 I-site; other site 316055011223 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 316055011224 amidase catalytic site [active] 316055011225 Zn binding residues [ion binding]; other site 316055011226 substrate binding site [chemical binding]; other site 316055011227 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 316055011228 Winged helix-turn helix; Region: HTH_29; pfam13551 316055011229 Helix-turn-helix domain; Region: HTH_28; pfam13518 316055011230 Homeodomain-like domain; Region: HTH_32; pfam13565 316055011231 DDE superfamily endonuclease; Region: DDE_3; pfam13358 316055011232 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 316055011233 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055011234 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055011235 Walker A/P-loop; other site 316055011236 ATP binding site [chemical binding]; other site 316055011237 Q-loop/lid; other site 316055011238 ABC transporter signature motif; other site 316055011239 Walker B; other site 316055011240 D-loop; other site 316055011241 H-loop/switch region; other site 316055011242 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 316055011243 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 316055011244 FtsX-like permease family; Region: FtsX; pfam02687 316055011245 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055011246 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055011247 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055011248 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055011249 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055011250 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 316055011251 catalytic site [active] 316055011252 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 316055011253 methionine sulfoxide reductase B; Provisional; Region: PRK00222 316055011254 SelR domain; Region: SelR; pfam01641 316055011255 methionine sulfoxide reductase A; Provisional; Region: PRK13014 316055011256 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 316055011257 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055011258 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 316055011259 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 316055011260 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316055011261 ATP-grasp domain; Region: ATP-grasp_4; cl17255 316055011262 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 316055011263 IMP binding site; other site 316055011264 dimer interface [polypeptide binding]; other site 316055011265 interdomain contacts; other site 316055011266 partial ornithine binding site; other site 316055011267 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 316055011268 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 316055011269 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 316055011270 Predicted membrane protein [Function unknown]; Region: COG2259 316055011271 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 316055011272 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 316055011273 putative DNA binding site [nucleotide binding]; other site 316055011274 putative Zn2+ binding site [ion binding]; other site 316055011275 AsnC family; Region: AsnC_trans_reg; pfam01037 316055011276 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 316055011277 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055011278 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055011279 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055011280 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055011281 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 316055011282 putative effector binding pocket; other site 316055011283 dimerization interface [polypeptide binding]; other site 316055011284 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 316055011285 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 316055011286 P-loop; other site 316055011287 Magnesium ion binding site [ion binding]; other site 316055011288 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; pfam01184 316055011289 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055011290 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055011291 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 316055011292 Walker A/P-loop; other site 316055011293 ATP binding site [chemical binding]; other site 316055011294 Q-loop/lid; other site 316055011295 ABC transporter signature motif; other site 316055011296 Walker B; other site 316055011297 D-loop; other site 316055011298 H-loop/switch region; other site 316055011299 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 316055011300 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055011301 active site 316055011302 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 316055011303 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 316055011304 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 316055011305 [2Fe-2S] cluster binding site [ion binding]; other site 316055011306 Predicted transcriptional regulators [Transcription]; Region: COG1695 316055011307 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 316055011308 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055011309 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055011310 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 316055011311 dimerization interface [polypeptide binding]; other site 316055011312 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 316055011313 peroxiredoxin; Provisional; Region: PRK13189 316055011314 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 316055011315 dimer interface [polypeptide binding]; other site 316055011316 decamer (pentamer of dimers) interface [polypeptide binding]; other site 316055011317 catalytic triad [active] 316055011318 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 316055011319 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 316055011320 CoenzymeA binding site [chemical binding]; other site 316055011321 subunit interaction site [polypeptide binding]; other site 316055011322 PHB binding site; other site 316055011323 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 316055011324 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 316055011325 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055011326 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055011327 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055011328 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055011329 osmolarity response regulator; Provisional; Region: ompR; PRK09468 316055011330 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 316055011331 active site 316055011332 phosphorylation site [posttranslational modification] 316055011333 intermolecular recognition site; other site 316055011334 dimerization interface [polypeptide binding]; other site 316055011335 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055011336 DNA binding site [nucleotide binding] 316055011337 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055011338 HAMP domain; Region: HAMP; pfam00672 316055011339 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055011340 dimer interface [polypeptide binding]; other site 316055011341 phosphorylation site [posttranslational modification] 316055011342 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 316055011343 ATP binding site [chemical binding]; other site 316055011344 Mg2+ binding site [ion binding]; other site 316055011345 G-X-G motif; other site 316055011346 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 316055011347 nucleophile elbow; other site 316055011348 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 316055011349 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055011350 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 316055011351 active site 316055011352 phosphorylation site [posttranslational modification] 316055011353 intermolecular recognition site; other site 316055011354 dimerization interface [polypeptide binding]; other site 316055011355 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055011356 DNA binding site [nucleotide binding] 316055011357 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 316055011358 active site 316055011359 DNA binding site [nucleotide binding] 316055011360 Int/Topo IB signature motif; other site 316055011361 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055011362 Phosphotransferase enzyme family; Region: APH; pfam01636 316055011363 Transposase domain (DUF772); Region: DUF772; pfam05598 316055011364 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 316055011365 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 316055011366 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 316055011367 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 316055011368 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055011369 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 316055011370 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 316055011371 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 316055011372 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 316055011373 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 316055011374 Transposase; Region: HTH_Tnp_1; pfam01527 316055011375 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 316055011376 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 316055011377 VirB7 interaction site; other site 316055011378 conjugal transfer protein TrbF; Provisional; Region: PRK13872 316055011379 conjugal transfer protein TrbL; Provisional; Region: PRK13875 316055011380 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 316055011381 conjugative transfer region protein TrbK; Region: other_trbK; TIGR04360 316055011382 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 316055011383 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 316055011384 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 316055011385 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 316055011386 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055011387 Walker A/P-loop; other site 316055011388 ATP binding site [chemical binding]; other site 316055011389 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 316055011390 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 316055011391 TrbC/VIRB2 family; Region: TrbC; pfam04956 316055011392 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 316055011393 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 316055011394 Walker A motif; other site 316055011395 ATP binding site [chemical binding]; other site 316055011396 Walker B motif; other site 316055011397 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 316055011398 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 316055011399 Walker A motif; other site 316055011400 ATP binding site [chemical binding]; other site 316055011401 Walker B motif; other site 316055011402 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 316055011403 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 316055011404 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 316055011405 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 316055011406 N-acetyl-D-glucosamine binding site [chemical binding]; other site 316055011407 catalytic residue [active] 316055011408 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 316055011409 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 316055011410 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 316055011411 Replication initiator protein A; Region: RPA; pfam10134 316055011412 Helix-turn-helix domain; Region: HTH_17; pfam12728 316055011413 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 316055011414 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055011415 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 316055011416 non-specific DNA binding site [nucleotide binding]; other site 316055011417 salt bridge; other site 316055011418 sequence-specific DNA binding site [nucleotide binding]; other site 316055011419 Uncharacterized conserved protein [Function unknown]; Region: COG5489 316055011420 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 316055011421 Toprim domain; Region: Toprim_3; pfam13362 316055011422 Methyltransferase domain; Region: Methyltransf_26; pfam13659 316055011423 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 316055011424 Helicase_C-like; Region: Helicase_C_4; pfam13871 316055011425 ParB-like nuclease domain; Region: ParBc; pfam02195 316055011426 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 316055011427 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 316055011428 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 316055011429 IHF dimer interface [polypeptide binding]; other site 316055011430 IHF - DNA interface [nucleotide binding]; other site 316055011431 DEAD-like helicases superfamily; Region: DEXDc; smart00487 316055011432 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 316055011433 ATP binding site [chemical binding]; other site 316055011434 putative Mg++ binding site [ion binding]; other site 316055011435 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 316055011436 nucleotide binding region [chemical binding]; other site 316055011437 ATP-binding site [chemical binding]; other site 316055011438 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 316055011439 generic binding surface I; other site 316055011440 generic binding surface II; other site 316055011441 Restriction endonuclease; Region: Mrr_cat; pfam04471 316055011442 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 316055011443 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 316055011444 Predicted ATPase [General function prediction only]; Region: COG4637 316055011445 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055011446 Walker A/P-loop; other site 316055011447 ATP binding site [chemical binding]; other site 316055011448 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 316055011449 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 316055011450 putative active site [active] 316055011451 putative metal-binding site [ion binding]; other site 316055011452 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 316055011453 Part of AAA domain; Region: AAA_19; pfam13245 316055011454 Family description; Region: UvrD_C_2; pfam13538 316055011455 Phasin protein; Region: Phasin_2; cl11491 316055011456 Phasin protein; Region: Phasin_2; cl11491 316055011457 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 316055011458 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 316055011459 putative active site [active] 316055011460 heme pocket [chemical binding]; other site 316055011461 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055011462 dimer interface [polypeptide binding]; other site 316055011463 phosphorylation site [posttranslational modification] 316055011464 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 316055011465 ATP binding site [chemical binding]; other site 316055011466 Mg2+ binding site [ion binding]; other site 316055011467 G-X-G motif; other site 316055011468 Rv0623-like transcription factor; Region: PSK_trans_fac; pfam07704 316055011469 PIN domain of the VapC-like UPF0110 protein Mb0640 and homologs; Region: PIN_UPF0110; cd09871 316055011470 putative active site [active] 316055011471 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055011472 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 316055011473 ligand binding site [chemical binding]; other site 316055011474 flexible hinge region; other site 316055011475 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 316055011476 putative switch regulator; other site 316055011477 non-specific DNA interactions [nucleotide binding]; other site 316055011478 DNA binding site [nucleotide binding] 316055011479 sequence specific DNA binding site [nucleotide binding]; other site 316055011480 putative cAMP binding site [chemical binding]; other site 316055011481 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055011482 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011483 dimer interface [polypeptide binding]; other site 316055011484 putative CheW interface [polypeptide binding]; other site 316055011485 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 316055011486 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 316055011487 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 316055011488 Multicopper oxidase; Region: Cu-oxidase; pfam00394 316055011489 Uncharacterized conserved protein [Function unknown]; Region: COG1262 316055011490 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 316055011491 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 316055011492 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 316055011493 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 316055011494 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055011495 dimer interface [polypeptide binding]; other site 316055011496 conserved gate region; other site 316055011497 putative PBP binding loops; other site 316055011498 ABC-ATPase subunit interface; other site 316055011499 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055011500 dimer interface [polypeptide binding]; other site 316055011501 putative PBP binding loops; other site 316055011502 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 316055011503 ABC-ATPase subunit interface; other site 316055011504 PAS fold; Region: PAS_3; pfam08447 316055011505 PAS domain; Region: PAS_9; pfam13426 316055011506 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055011507 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 316055011508 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055011509 dimer interface [polypeptide binding]; other site 316055011510 phosphorylation site [posttranslational modification] 316055011511 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 316055011512 ATP binding site [chemical binding]; other site 316055011513 Mg2+ binding site [ion binding]; other site 316055011514 G-X-G motif; other site 316055011515 Response regulator receiver domain; Region: Response_reg; pfam00072 316055011516 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 316055011517 active site 316055011518 phosphorylation site [posttranslational modification] 316055011519 intermolecular recognition site; other site 316055011520 dimerization interface [polypeptide binding]; other site 316055011521 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 316055011522 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 316055011523 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 316055011524 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 316055011525 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 316055011526 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055011527 dimer interface [polypeptide binding]; other site 316055011528 conserved gate region; other site 316055011529 putative PBP binding loops; other site 316055011530 ABC-ATPase subunit interface; other site 316055011531 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055011532 dimer interface [polypeptide binding]; other site 316055011533 conserved gate region; other site 316055011534 putative PBP binding loops; other site 316055011535 ABC-ATPase subunit interface; other site 316055011536 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 316055011537 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055011538 Walker A/P-loop; other site 316055011539 ATP binding site [chemical binding]; other site 316055011540 Q-loop/lid; other site 316055011541 ABC transporter signature motif; other site 316055011542 Walker B; other site 316055011543 D-loop; other site 316055011544 H-loop/switch region; other site 316055011545 TOBE domain; Region: TOBE_2; pfam08402 316055011546 PAS domain; Region: PAS; smart00091 316055011547 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 316055011548 putative active site [active] 316055011549 PAS domain; Region: PAS; smart00091 316055011550 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 316055011551 putative active site [active] 316055011552 heme pocket [chemical binding]; other site 316055011553 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055011554 metal binding site [ion binding]; metal-binding site 316055011555 active site 316055011556 I-site; other site 316055011557 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 316055011558 hydroxyglutarate oxidase; Provisional; Region: PRK11728 316055011559 Predicted dehydrogenase [General function prediction only]; Region: COG0579 316055011560 Uncharacterized small protein [Function unknown]; Region: COG5570 316055011561 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]; Region: COG5481 316055011562 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055011563 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055011564 metal binding site [ion binding]; metal-binding site 316055011565 active site 316055011566 I-site; other site 316055011567 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 316055011568 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 316055011569 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 316055011570 ATP-grasp domain; Region: ATP-grasp; pfam02222 316055011571 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 316055011572 PilZ domain; Region: PilZ; pfam07238 316055011573 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055011574 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 316055011575 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 316055011576 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 316055011577 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 316055011578 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 316055011579 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 316055011580 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 316055011581 ligand binding site [chemical binding]; other site 316055011582 homodimer interface [polypeptide binding]; other site 316055011583 NAD(P) binding site [chemical binding]; other site 316055011584 trimer interface B [polypeptide binding]; other site 316055011585 trimer interface A [polypeptide binding]; other site 316055011586 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 316055011587 Fic/DOC family; Region: Fic; cl00960 316055011588 putative addiction module antidote; Region: doc_partner; TIGR02609 316055011589 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 316055011590 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 316055011591 active site 316055011592 Zn binding site [ion binding]; other site 316055011593 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 316055011594 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 316055011595 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 316055011596 active site 316055011597 phosphorylation site [posttranslational modification] 316055011598 intermolecular recognition site; other site 316055011599 dimerization interface [polypeptide binding]; other site 316055011600 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055011601 Walker A motif; other site 316055011602 ATP binding site [chemical binding]; other site 316055011603 Walker B motif; other site 316055011604 arginine finger; other site 316055011605 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055011606 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 316055011607 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316055011608 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055011609 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055011610 Bacterial protein of unknown function (DUF882); Region: Peptidase_M15_2; pfam05951 316055011611 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 316055011612 hypothetical protein; Provisional; Region: PRK13694 316055011613 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3492 316055011614 Protein of unknown function (DUF1036); Region: DUF1036; pfam06282 316055011615 pyruvate kinase; Provisional; Region: PRK06247 316055011616 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 316055011617 domain interfaces; other site 316055011618 active site 316055011619 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 316055011620 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 316055011621 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055011622 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 316055011623 binding surface 316055011624 TPR motif; other site 316055011625 TPR repeat; Region: TPR_11; pfam13414 316055011626 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 316055011627 (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 316055011628 active site 316055011629 catalytic site [active] 316055011630 (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 316055011631 active site 316055011632 catalytic site [active] 316055011633 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 316055011634 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 316055011635 Bacterial transcriptional regulator; Region: IclR; pfam01614 316055011636 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cd01292 316055011637 active site 316055011638 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 316055011639 putative deacylase active site [active] 316055011640 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 316055011641 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 316055011642 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055011643 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 316055011644 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 316055011645 active site 316055011646 enoyl-CoA hydratase; Provisional; Region: PRK06494 316055011647 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 316055011648 substrate binding site [chemical binding]; other site 316055011649 oxyanion hole (OAH) forming residues; other site 316055011650 trimer interface [polypeptide binding]; other site 316055011651 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 316055011652 RNA/DNA hybrid binding site [nucleotide binding]; other site 316055011653 active site 316055011654 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 316055011655 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 316055011656 putative active site [active] 316055011657 putative substrate binding site [chemical binding]; other site 316055011658 ATP binding site [chemical binding]; other site 316055011659 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 316055011660 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 316055011661 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3820 316055011662 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 316055011663 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055011664 prevent-host-death family protein; Region: phd_fam; TIGR01552 316055011665 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 316055011666 oligomeric interface; other site 316055011667 putative active site [active] 316055011668 homodimer interface [polypeptide binding]; other site 316055011669 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 316055011670 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 316055011671 GDP-binding site [chemical binding]; other site 316055011672 ACT binding site; other site 316055011673 IMP binding site; other site 316055011674 Motility quorum-sensing regulator (MqsR); Region: MqsR; cd12869 316055011675 peptide binding site [polypeptide binding]; other site 316055011676 YgiT-type zinc finger domain; Region: YgiT_finger; TIGR03831 316055011677 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 316055011678 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 316055011679 non-specific DNA binding site [nucleotide binding]; other site 316055011680 salt bridge; other site 316055011681 sequence-specific DNA binding site [nucleotide binding]; other site 316055011682 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 316055011683 trimethylamine N-oxide reductase cytochrome c-type subunit; Provisional; Region: PRK15032 316055011684 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 316055011685 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 316055011686 PAS fold; Region: PAS_7; pfam12860 316055011687 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055011688 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055011689 metal binding site [ion binding]; metal-binding site 316055011690 active site 316055011691 I-site; other site 316055011692 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 316055011693 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 316055011694 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055011695 Beta-Casp domain; Region: Beta-Casp; smart01027 316055011696 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 316055011697 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 316055011698 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 316055011699 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055011700 active site 316055011701 thymidine phosphorylase; Provisional; Region: PRK04350 316055011702 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 316055011703 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 316055011704 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 316055011705 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 316055011706 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 316055011707 active site 316055011708 catalytic tetrad [active] 316055011709 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 316055011710 putative deacylase active site [active] 316055011711 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 316055011712 EamA-like transporter family; Region: EamA; pfam00892 316055011713 EamA-like transporter family; Region: EamA; pfam00892 316055011714 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 316055011715 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055011716 putative active site [active] 316055011717 heme pocket [chemical binding]; other site 316055011718 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055011719 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 316055011720 putative active site [active] 316055011721 heme pocket [chemical binding]; other site 316055011722 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 316055011723 putative active site [active] 316055011724 heme pocket [chemical binding]; other site 316055011725 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011726 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055011727 dimer interface [polypeptide binding]; other site 316055011728 putative CheW interface [polypeptide binding]; other site 316055011729 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055011730 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011731 dimer interface [polypeptide binding]; other site 316055011732 putative CheW interface [polypeptide binding]; other site 316055011733 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 316055011734 diiron binding motif [ion binding]; other site 316055011735 Uncharacterized conserved protein [Function unknown]; Region: COG1633 316055011736 CCC1-related family of proteins; Region: CCC1_like; cl00278 316055011737 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 316055011738 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055011739 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055011740 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055011741 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011742 dimer interface [polypeptide binding]; other site 316055011743 putative CheW interface [polypeptide binding]; other site 316055011744 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 316055011745 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055011746 dimerization interface [polypeptide binding]; other site 316055011747 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011748 dimer interface [polypeptide binding]; other site 316055011749 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055011750 putative CheW interface [polypeptide binding]; other site 316055011751 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 316055011752 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 316055011753 ligand binding site [chemical binding]; other site 316055011754 NAD binding site [chemical binding]; other site 316055011755 dimerization interface [polypeptide binding]; other site 316055011756 catalytic site [active] 316055011757 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 316055011758 putative L-serine binding site [chemical binding]; other site 316055011759 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; cd01494 316055011760 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055011761 catalytic residue [active] 316055011762 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055011763 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055011764 Coenzyme A binding pocket [chemical binding]; other site 316055011765 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055011766 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 316055011767 putative C-terminal domain interface [polypeptide binding]; other site 316055011768 putative GSH binding site (G-site) [chemical binding]; other site 316055011769 putative dimer interface [polypeptide binding]; other site 316055011770 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 316055011771 dimer interface [polypeptide binding]; other site 316055011772 N-terminal domain interface [polypeptide binding]; other site 316055011773 substrate binding pocket (H-site) [chemical binding]; other site 316055011774 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055011775 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055011776 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 316055011777 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055011778 putative substrate translocation pore; other site 316055011779 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 316055011780 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 316055011781 active site 316055011782 substrate binding site [chemical binding]; other site 316055011783 metal binding site [ion binding]; metal-binding site 316055011784 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 316055011785 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 316055011786 active site 316055011787 substrate binding site [chemical binding]; other site 316055011788 FMN binding site [chemical binding]; other site 316055011789 putative catalytic residues [active] 316055011790 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 316055011791 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 316055011792 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 316055011793 shikimate binding site; other site 316055011794 NAD(P) binding site [chemical binding]; other site 316055011795 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055011796 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 316055011797 non-specific DNA binding site [nucleotide binding]; other site 316055011798 salt bridge; other site 316055011799 sequence-specific DNA binding site [nucleotide binding]; other site 316055011800 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 316055011801 elongation factor G; Reviewed; Region: PRK12740 316055011802 G1 box; other site 316055011803 putative GEF interaction site [polypeptide binding]; other site 316055011804 GTP/Mg2+ binding site [chemical binding]; other site 316055011805 Switch I region; other site 316055011806 G2 box; other site 316055011807 G3 box; other site 316055011808 Switch II region; other site 316055011809 G4 box; other site 316055011810 G5 box; other site 316055011811 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 316055011812 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 316055011813 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 316055011814 Protein of unknown function (DUF992); Region: DUF992; pfam06186 316055011815 Protein of unknown function (DUF992); Region: DUF992; pfam06186 316055011816 aspartate aminotransferase; Provisional; Region: PRK05764 316055011817 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 316055011818 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055011819 homodimer interface [polypeptide binding]; other site 316055011820 catalytic residue [active] 316055011821 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055011822 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 316055011823 putative C-terminal domain interface [polypeptide binding]; other site 316055011824 putative GSH binding site (G-site) [chemical binding]; other site 316055011825 putative dimer interface [polypeptide binding]; other site 316055011826 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 316055011827 N-terminal domain interface [polypeptide binding]; other site 316055011828 dimer interface [polypeptide binding]; other site 316055011829 substrate binding pocket (H-site) [chemical binding]; other site 316055011830 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 316055011831 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 316055011832 Protein of unknown function, DUF486; Region: DUF486; cl01236 316055011833 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 316055011834 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 316055011835 putative acyl-acceptor binding pocket; other site 316055011836 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 316055011837 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 316055011838 active site 316055011839 catalytic tetrad [active] 316055011840 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316055011841 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 316055011842 motif II; other site 316055011843 GST_N family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as...; Region: GST_N_etherase_LigE; cd03038 316055011844 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055011845 putative C-terminal domain interface [polypeptide binding]; other site 316055011846 putative GSH binding site (G-site) [chemical binding]; other site 316055011847 putative dimer interface [polypeptide binding]; other site 316055011848 C-terminal, alpha helical domain of Beta etherase LigE; Region: GST_C_etherase_LigE; cd03202 316055011849 putative N-terminal domain interface [polypeptide binding]; other site 316055011850 putative dimer interface [polypeptide binding]; other site 316055011851 putative substrate binding pocket (H-site) [chemical binding]; other site 316055011852 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 316055011853 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 316055011854 C-terminal domain interface [polypeptide binding]; other site 316055011855 GSH binding site (G-site) [chemical binding]; other site 316055011856 dimer interface [polypeptide binding]; other site 316055011857 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 316055011858 N-terminal domain interface [polypeptide binding]; other site 316055011859 putative dimer interface [polypeptide binding]; other site 316055011860 active site 316055011861 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 316055011862 pseudo EF-hand loop; other site 316055011863 peptide binding pocket; other site 316055011864 Ca2+ binding site [ion binding]; other site 316055011865 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 316055011866 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055011867 excinuclease ABC subunit B; Provisional; Region: PRK05298 316055011868 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 316055011869 ATP binding site [chemical binding]; other site 316055011870 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 316055011871 nucleotide binding region [chemical binding]; other site 316055011872 ATP-binding site [chemical binding]; other site 316055011873 Ultra-violet resistance protein B; Region: UvrB; pfam12344 316055011874 UvrB/uvrC motif; Region: UVR; pfam02151 316055011875 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 316055011876 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 316055011877 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 316055011878 Domain of unknown function (DUF1902); Region: DUF1902; pfam08972 316055011879 YcfA-like protein; Region: YcfA; pfam07927 316055011880 acetyl-CoA acetyltransferase; Provisional; Region: PRK06025 316055011881 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 316055011882 dimer interface [polypeptide binding]; other site 316055011883 active site 316055011884 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055011885 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055011886 dimer interface [polypeptide binding]; other site 316055011887 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055011888 putative CheW interface [polypeptide binding]; other site 316055011889 NADH(P)-binding; Region: NAD_binding_10; pfam13460 316055011890 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055011891 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055011892 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 316055011893 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 316055011894 homotetramer interface [polypeptide binding]; other site 316055011895 ligand binding site [chemical binding]; other site 316055011896 catalytic site [active] 316055011897 NAD binding site [chemical binding]; other site 316055011898 S-adenosylmethionine synthetase; Validated; Region: PRK05250 316055011899 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 316055011900 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 316055011901 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 316055011902 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 316055011903 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 316055011904 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316055011905 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 316055011906 TPR repeat; Region: TPR_11; pfam13414 316055011907 TPR repeat; Region: TPR_11; pfam13414 316055011908 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 316055011909 binding surface 316055011910 TPR motif; other site 316055011911 TPR repeat; Region: TPR_11; pfam13414 316055011912 Caspase domain; Region: Peptidase_C14; pfam00656 316055011913 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 316055011914 substrate binding site [chemical binding]; other site 316055011915 THF binding site; other site 316055011916 zinc-binding site [ion binding]; other site 316055011917 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055011918 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055011919 Walker A/P-loop; other site 316055011920 ATP binding site [chemical binding]; other site 316055011921 Q-loop/lid; other site 316055011922 ABC transporter signature motif; other site 316055011923 Walker B; other site 316055011924 D-loop; other site 316055011925 H-loop/switch region; other site 316055011926 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055011927 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055011928 Walker A/P-loop; other site 316055011929 ATP binding site [chemical binding]; other site 316055011930 Q-loop/lid; other site 316055011931 ABC transporter signature motif; other site 316055011932 Walker B; other site 316055011933 D-loop; other site 316055011934 H-loop/switch region; other site 316055011935 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 316055011936 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055011937 TM-ABC transporter signature motif; other site 316055011938 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055011939 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 316055011940 TM-ABC transporter signature motif; other site 316055011941 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 316055011942 Transposase; Region: DEDD_Tnp_IS110; pfam01548 316055011943 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 316055011944 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055011945 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 316055011946 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 316055011947 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 316055011948 Mg++ binding site [ion binding]; other site 316055011949 putative catalytic motif [active] 316055011950 putative substrate binding site [chemical binding]; other site 316055011951 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 316055011952 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 316055011953 NAD(P) binding site [chemical binding]; other site 316055011954 homodimer interface [polypeptide binding]; other site 316055011955 substrate binding site [chemical binding]; other site 316055011956 active site 316055011957 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 316055011958 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 316055011959 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 316055011960 putative active site [active] 316055011961 putative substrate binding site [chemical binding]; other site 316055011962 putative cosubstrate binding site; other site 316055011963 catalytic site [active] 316055011964 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 316055011965 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 316055011966 active site 316055011967 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055011968 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 316055011969 putative ligand binding site [chemical binding]; other site 316055011970 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 316055011971 TM-ABC transporter signature motif; other site 316055011972 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055011973 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 316055011974 TM-ABC transporter signature motif; other site 316055011975 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055011976 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055011977 Walker A/P-loop; other site 316055011978 ATP binding site [chemical binding]; other site 316055011979 Q-loop/lid; other site 316055011980 ABC transporter signature motif; other site 316055011981 Walker B; other site 316055011982 D-loop; other site 316055011983 H-loop/switch region; other site 316055011984 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055011985 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055011986 Walker A/P-loop; other site 316055011987 ATP binding site [chemical binding]; other site 316055011988 Q-loop/lid; other site 316055011989 ABC transporter signature motif; other site 316055011990 Walker B; other site 316055011991 D-loop; other site 316055011992 H-loop/switch region; other site 316055011993 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 316055011994 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055011995 Walker A/P-loop; other site 316055011996 ATP binding site [chemical binding]; other site 316055011997 Q-loop/lid; other site 316055011998 ABC transporter signature motif; other site 316055011999 Walker B; other site 316055012000 D-loop; other site 316055012001 H-loop/switch region; other site 316055012002 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 316055012003 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055012004 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 316055012005 acyl-activating enzyme (AAE) consensus motif; other site 316055012006 putative AMP binding site [chemical binding]; other site 316055012007 putative active site [active] 316055012008 putative CoA binding site [chemical binding]; other site 316055012009 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316055012010 putative active site [active] 316055012011 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055012012 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 316055012013 TM-ABC transporter signature motif; other site 316055012014 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 316055012015 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 316055012016 TM-ABC transporter signature motif; other site 316055012017 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055012018 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 316055012019 putative ligand binding site [chemical binding]; other site 316055012020 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 316055012021 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055012022 Walker A/P-loop; other site 316055012023 ATP binding site [chemical binding]; other site 316055012024 Q-loop/lid; other site 316055012025 ABC transporter signature motif; other site 316055012026 Walker B; other site 316055012027 D-loop; other site 316055012028 H-loop/switch region; other site 316055012029 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 316055012030 putative ADP-binding pocket [chemical binding]; other site 316055012031 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055012032 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 316055012033 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 316055012034 NAD(P) binding site [chemical binding]; other site 316055012035 catalytic residues [active] 316055012036 flagellin modification protein A; Provisional; Region: PRK09186 316055012037 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055012038 NAD(P) binding site [chemical binding]; other site 316055012039 active site 316055012040 Sialic acid synthase [Cell envelope biogenesis, outer membrane]; Region: SpsE; COG2089 316055012041 NeuB family; Region: NeuB; pfam03102 316055012042 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 316055012043 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 316055012044 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 316055012045 TPP-binding site [chemical binding]; other site 316055012046 dimer interface [polypeptide binding]; other site 316055012047 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 316055012048 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 316055012049 PYR/PP interface [polypeptide binding]; other site 316055012050 dimer interface [polypeptide binding]; other site 316055012051 TPP binding site [chemical binding]; other site 316055012052 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055012053 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 316055012054 ligand binding site; other site 316055012055 tetramer interface; other site 316055012056 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 316055012057 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 316055012058 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055012059 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 316055012060 Methyltransferase domain; Region: Methyltransf_24; pfam13578 316055012061 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055012062 active site 316055012063 Cephalosporin hydroxylase; Region: CmcI; pfam04989 316055012064 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 316055012065 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 316055012066 active site 316055012067 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 316055012068 S-adenosylmethionine binding site [chemical binding]; other site 316055012069 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 316055012070 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 316055012071 Walker A/P-loop; other site 316055012072 ATP binding site [chemical binding]; other site 316055012073 Q-loop/lid; other site 316055012074 ABC transporter signature motif; other site 316055012075 Walker B; other site 316055012076 D-loop; other site 316055012077 H-loop/switch region; other site 316055012078 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 316055012079 putative carbohydrate binding site [chemical binding]; other site 316055012080 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 316055012081 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055012082 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 316055012083 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 316055012084 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 316055012085 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 316055012086 inhibitor-cofactor binding pocket; inhibition site 316055012087 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055012088 catalytic residue [active] 316055012089 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 316055012090 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 316055012091 substrate binding site; other site 316055012092 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 316055012093 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 316055012094 NAD binding site [chemical binding]; other site 316055012095 homotetramer interface [polypeptide binding]; other site 316055012096 homodimer interface [polypeptide binding]; other site 316055012097 substrate binding site [chemical binding]; other site 316055012098 active site 316055012099 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 316055012100 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055012101 Methyltransferase domain; Region: Methyltransf_12; pfam08242 316055012102 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 316055012103 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 316055012104 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 316055012105 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 316055012106 putative trimer interface [polypeptide binding]; other site 316055012107 putative CoA binding site [chemical binding]; other site 316055012108 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 316055012109 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316055012110 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 316055012111 NADP-binding site; other site 316055012112 homotetramer interface [polypeptide binding]; other site 316055012113 substrate binding site [chemical binding]; other site 316055012114 homodimer interface [polypeptide binding]; other site 316055012115 active site 316055012116 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 316055012117 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 316055012118 NADP-binding site; other site 316055012119 homotetramer interface [polypeptide binding]; other site 316055012120 substrate binding site [chemical binding]; other site 316055012121 homodimer interface [polypeptide binding]; other site 316055012122 active site 316055012123 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 316055012124 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055012125 putative substrate translocation pore; other site 316055012126 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 316055012127 FHIPEP family; Region: FHIPEP; pfam00771 316055012128 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 316055012129 Anti-sigma-K factor rskA; Region: RskA; pfam10099 316055012130 RNA polymerase sigma factor; Provisional; Region: PRK12514 316055012131 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055012132 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055012133 DNA binding residues [nucleotide binding] 316055012134 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 316055012135 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 316055012136 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 316055012137 Walker A motif/ATP binding site; other site 316055012138 Walker B motif; other site 316055012139 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055012140 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 316055012141 active site 316055012142 phosphorylation site [posttranslational modification] 316055012143 intermolecular recognition site; other site 316055012144 dimerization interface [polypeptide binding]; other site 316055012145 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055012146 DNA binding site [nucleotide binding] 316055012147 UDP-glucose 4-epimerase; Region: PLN02240 316055012148 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 316055012149 NAD binding site [chemical binding]; other site 316055012150 homodimer interface [polypeptide binding]; other site 316055012151 active site 316055012152 substrate binding site [chemical binding]; other site 316055012153 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 316055012154 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 316055012155 Substrate binding site; other site 316055012156 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 316055012157 Predicted membrane protein [Function unknown]; Region: COG2246 316055012158 GtrA-like protein; Region: GtrA; pfam04138 316055012159 LysE type translocator; Region: LysE; cl00565 316055012160 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 316055012161 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 316055012162 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 316055012163 PAS domain; Region: PAS_9; pfam13426 316055012164 putative active site [active] 316055012165 heme pocket [chemical binding]; other site 316055012166 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055012167 dimerization interface [polypeptide binding]; other site 316055012168 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055012169 dimer interface [polypeptide binding]; other site 316055012170 putative CheW interface [polypeptide binding]; other site 316055012171 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 316055012172 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 316055012173 active site 316055012174 substrate binding site [chemical binding]; other site 316055012175 metal binding site [ion binding]; metal-binding site 316055012176 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 316055012177 dimerization interface [polypeptide binding]; other site 316055012178 putative active cleft [active] 316055012179 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316055012180 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 316055012181 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 316055012182 S-adenosylmethionine binding site [chemical binding]; other site 316055012183 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 316055012184 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 316055012185 active site 316055012186 phosphorylation site [posttranslational modification] 316055012187 intermolecular recognition site; other site 316055012188 dimerization interface [polypeptide binding]; other site 316055012189 CheB methylesterase; Region: CheB_methylest; pfam01339 316055012190 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 316055012191 Response regulator receiver domain; Region: Response_reg; pfam00072 316055012192 active site 316055012193 phosphorylation site [posttranslational modification] 316055012194 intermolecular recognition site; other site 316055012195 dimerization interface [polypeptide binding]; other site 316055012196 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 316055012197 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 316055012198 putative binding surface; other site 316055012199 active site 316055012200 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 316055012201 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316055012202 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 316055012203 ATP binding site [chemical binding]; other site 316055012204 Mg2+ binding site [ion binding]; other site 316055012205 G-X-G motif; other site 316055012206 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 316055012207 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055012208 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 316055012209 active site 316055012210 phosphorylation site [posttranslational modification] 316055012211 intermolecular recognition site; other site 316055012212 dimerization interface [polypeptide binding]; other site 316055012213 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 316055012214 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 316055012215 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 316055012216 active site 316055012217 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 316055012218 Protein of unknown function (DUF1134); Region: DUF1134; pfam06577 316055012219 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 316055012220 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316055012221 metal binding site 2 [ion binding]; metal-binding site 316055012222 putative DNA binding helix; other site 316055012223 metal binding site 1 [ion binding]; metal-binding site 316055012224 dimer interface [polypeptide binding]; other site 316055012225 structural Zn2+ binding site [ion binding]; other site 316055012226 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 316055012227 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 316055012228 Walker A/P-loop; other site 316055012229 ATP binding site [chemical binding]; other site 316055012230 Q-loop/lid; other site 316055012231 ABC transporter signature motif; other site 316055012232 Walker B; other site 316055012233 D-loop; other site 316055012234 H-loop/switch region; other site 316055012235 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 316055012236 cobalt transport protein CbiM; Validated; Region: PRK06265 316055012237 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 316055012238 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 316055012239 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 316055012240 CrcB-like protein; Region: CRCB; cl09114 316055012241 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 316055012242 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 316055012243 hypothetical protein; Validated; Region: PRK07586 316055012244 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055012245 PYR/PP interface [polypeptide binding]; other site 316055012246 dimer interface [polypeptide binding]; other site 316055012247 TPP binding site [chemical binding]; other site 316055012248 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 316055012249 TPP-binding site [chemical binding]; other site 316055012250 dimer interface [polypeptide binding]; other site 316055012251 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055012252 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055012253 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 316055012254 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 316055012255 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 316055012256 benzoylformate decarboxylase; Reviewed; Region: PRK07092 316055012257 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316055012258 PYR/PP interface [polypeptide binding]; other site 316055012259 dimer interface [polypeptide binding]; other site 316055012260 TPP binding site [chemical binding]; other site 316055012261 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316055012262 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 316055012263 TPP-binding site [chemical binding]; other site 316055012264 dimer interface [polypeptide binding]; other site 316055012265 Uncharacterized conserved protein [Function unknown]; Region: COG3777 316055012266 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 316055012267 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 316055012268 active site 2 [active] 316055012269 active site 1 [active] 316055012270 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 316055012271 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055012272 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055012273 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316055012274 active site 316055012275 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 316055012276 Cytochrome P450; Region: p450; cl12078 316055012277 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 316055012278 isovaleryl-CoA dehydrogenase; Region: PLN02519 316055012279 substrate binding site [chemical binding]; other site 316055012280 FAD binding site [chemical binding]; other site 316055012281 catalytic base [active] 316055012282 classical (c) SDRs; Region: SDR_c; cd05233 316055012283 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 316055012284 NAD(P) binding site [chemical binding]; other site 316055012285 active site 316055012286 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 316055012287 YcjX-like family, DUF463; Region: DUF463; pfam04317 316055012288 hypothetical protein; Provisional; Region: PRK05415 316055012289 Domain of unknown function (DUF697); Region: DUF697; cl12064 316055012290 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 316055012291 DNA-binding site [nucleotide binding]; DNA binding site 316055012292 RNA-binding motif; other site 316055012293 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 316055012294 Proline dehydrogenase; Region: Pro_dh; pfam01619 316055012295 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 316055012296 Glutamate binding site [chemical binding]; other site 316055012297 NAD binding site [chemical binding]; other site 316055012298 catalytic residues [active] 316055012299 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 316055012300 CoA-transferase family III; Region: CoA_transf_3; pfam02515 316055012301 Repair protein; Region: Repair_PSII; pfam04536 316055012302 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 316055012303 Repair protein; Region: Repair_PSII; pfam04536 316055012304 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 316055012305 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316055012306 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055012307 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055012308 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 316055012309 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055012310 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055012311 acyl-activating enzyme (AAE) consensus motif; other site 316055012312 acyl-activating enzyme (AAE) consensus motif; other site 316055012313 putative AMP binding site [chemical binding]; other site 316055012314 putative active site [active] 316055012315 putative CoA binding site [chemical binding]; other site 316055012316 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 316055012317 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 316055012318 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 316055012319 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316055012320 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 316055012321 putative C-terminal domain interface [polypeptide binding]; other site 316055012322 putative GSH binding site (G-site) [chemical binding]; other site 316055012323 putative dimer interface [polypeptide binding]; other site 316055012324 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 316055012325 dimer interface [polypeptide binding]; other site 316055012326 N-terminal domain interface [polypeptide binding]; other site 316055012327 putative substrate binding pocket (H-site) [chemical binding]; other site 316055012328 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 316055012329 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 316055012330 DNA binding site [nucleotide binding] 316055012331 active site 316055012332 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055012333 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 316055012334 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316055012335 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 316055012336 O-Antigen ligase; Region: Wzy_C; pfam04932 316055012337 Uncharacterized bacterial family of heme peroxidases; Region: An_peroxidase_bacterial_1; cd09819 316055012338 putative heme binding site [chemical binding]; other site 316055012339 putative substrate binding site [chemical binding]; other site 316055012340 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 316055012341 Peptidase family M23; Region: Peptidase_M23; pfam01551 316055012342 Uncharacterized conserved protein [Function unknown]; Region: COG3391 316055012343 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 316055012344 Clp amino terminal domain; Region: Clp_N; pfam02861 316055012345 Clp amino terminal domain; Region: Clp_N; pfam02861 316055012346 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055012347 Walker A motif; other site 316055012348 ATP binding site [chemical binding]; other site 316055012349 Walker B motif; other site 316055012350 arginine finger; other site 316055012351 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055012352 Walker A motif; other site 316055012353 ATP binding site [chemical binding]; other site 316055012354 Walker B motif; other site 316055012355 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 316055012356 TIGR02594 family protein; Region: TIGR02594 316055012357 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055012358 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 316055012359 S-adenosylmethionine binding site [chemical binding]; other site 316055012360 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 316055012361 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 316055012362 hypothetical protein; Provisional; Region: PRK06034 316055012363 Chorismate mutase type II; Region: CM_2; pfam01817 316055012364 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 316055012365 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 316055012366 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055012367 homodimer interface [polypeptide binding]; other site 316055012368 catalytic residue [active] 316055012369 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 316055012370 prephenate dehydrogenase; Validated; Region: PRK08507 316055012371 Cupin domain; Region: Cupin_2; pfam07883 316055012372 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 316055012373 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055012374 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 316055012375 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 316055012376 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 316055012377 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 316055012378 Cl binding site [ion binding]; other site 316055012379 oligomer interface [polypeptide binding]; other site 316055012380 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 316055012381 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316055012382 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 316055012383 putative acyl-CoA synthetase; Provisional; Region: PRK06018 316055012384 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 316055012385 dimer interface [polypeptide binding]; other site 316055012386 acyl-activating enzyme (AAE) consensus motif; other site 316055012387 putative active site [active] 316055012388 AMP binding site [chemical binding]; other site 316055012389 putative CoA binding site [chemical binding]; other site 316055012390 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316055012391 putative active site [active] 316055012392 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 316055012393 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 316055012394 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 316055012395 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 316055012396 FAD binding site [chemical binding]; other site 316055012397 substrate binding pocket [chemical binding]; other site 316055012398 catalytic base [active] 316055012399 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 316055012400 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 316055012401 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 316055012402 dimerization interface [polypeptide binding]; other site 316055012403 active site 316055012404 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 316055012405 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 316055012406 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055012407 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 316055012408 ligand binding site [chemical binding]; other site 316055012409 flexible hinge region; other site 316055012410 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 316055012411 non-specific DNA interactions [nucleotide binding]; other site 316055012412 DNA binding site [nucleotide binding] 316055012413 sequence specific DNA binding site [nucleotide binding]; other site 316055012414 putative cAMP binding site [chemical binding]; other site 316055012415 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 316055012416 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055012417 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 316055012418 protein binding site [polypeptide binding]; other site 316055012419 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 316055012420 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 316055012421 non-specific DNA binding site [nucleotide binding]; other site 316055012422 salt bridge; other site 316055012423 sequence-specific DNA binding site [nucleotide binding]; other site 316055012424 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 316055012425 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 316055012426 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 316055012427 molybdenum transport protein ModD; Provisional; Region: PRK06096 316055012428 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl17275 316055012429 active site 316055012430 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 316055012431 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 316055012432 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 316055012433 ArsC family; Region: ArsC; pfam03960 316055012434 putative catalytic residues [active] 316055012435 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 316055012436 putative metal binding site [ion binding]; other site 316055012437 Uncharacterized conserved protein [Function unknown]; Region: COG1432 316055012438 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 316055012439 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 316055012440 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 316055012441 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 316055012442 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055012443 ligand binding site [chemical binding]; other site 316055012444 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 316055012445 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055012446 Acetoacetate decarboxylase (ADC); Region: ADC; cl01919 316055012447 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 316055012448 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055012449 cyclase homology domain; Region: CHD; cd07302 316055012450 nucleotidyl binding site; other site 316055012451 metal binding site [ion binding]; metal-binding site 316055012452 dimer interface [polypeptide binding]; other site 316055012453 cyclase homology domain; Region: CHD; cd07302 316055012454 dimer interface [polypeptide binding]; other site 316055012455 nucleotidyl binding site; other site 316055012456 metal binding site [ion binding]; metal-binding site 316055012457 Predicted ATPase [General function prediction only]; Region: COG3899 316055012458 AAA ATPase domain; Region: AAA_16; pfam13191 316055012459 UDP-glucose 4-epimerase; Region: PLN02240 316055012460 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 316055012461 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 316055012462 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 316055012463 FAD binding domain; Region: FAD_binding_4; pfam01565 316055012464 AAA ATPase domain; Region: AAA_16; pfam13191 316055012465 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 316055012466 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_15; cd04673 316055012467 nudix motif; other site 316055012468 TIGR02301 family protein; Region: TIGR02301 316055012469 Transposase domain (DUF772); Region: DUF772; pfam05598 316055012470 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055012471 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 316055012472 dihydroorotase; Validated; Region: PRK09060 316055012473 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 316055012474 active site 316055012475 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 316055012476 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 316055012477 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 316055012478 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 316055012479 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 316055012480 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG5350 316055012481 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 316055012482 FecR protein; Region: FecR; pfam04773 316055012483 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 316055012484 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055012485 cyclase homology domain; Region: CHD; cd07302 316055012486 nucleotidyl binding site; other site 316055012487 metal binding site [ion binding]; metal-binding site 316055012488 dimer interface [polypeptide binding]; other site 316055012489 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 316055012490 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 316055012491 NADP binding site [chemical binding]; other site 316055012492 dimer interface [polypeptide binding]; other site 316055012493 quinolinate synthetase; Provisional; Region: PRK09375 316055012494 L-aspartate oxidase; Provisional; Region: PRK07512 316055012495 L-aspartate oxidase; Provisional; Region: PRK06175 316055012496 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 316055012497 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 316055012498 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 316055012499 dimerization interface [polypeptide binding]; other site 316055012500 active site 316055012501 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 316055012502 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 316055012503 pyruvate phosphate dikinase; Provisional; Region: PRK09279 316055012504 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 316055012505 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 316055012506 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 316055012507 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 316055012508 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 316055012509 DALR anticodon binding domain; Region: DALR_1; pfam05746 316055012510 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316055012511 putative active site [active] 316055012512 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 316055012513 dimer interface [polypeptide binding]; other site 316055012514 motif 1; other site 316055012515 active site 316055012516 motif 2; other site 316055012517 motif 3; other site 316055012518 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 316055012519 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 316055012520 tandem repeat interface [polypeptide binding]; other site 316055012521 oligomer interface [polypeptide binding]; other site 316055012522 active site residues [active] 316055012523 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 316055012524 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 316055012525 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 316055012526 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 316055012527 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 316055012528 substrate binding pocket [chemical binding]; other site 316055012529 chain length determination region; other site 316055012530 substrate-Mg2+ binding site; other site 316055012531 catalytic residues [active] 316055012532 aspartate-rich region 1; other site 316055012533 active site lid residues [active] 316055012534 aspartate-rich region 2; other site 316055012535 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 316055012536 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 316055012537 binding surface 316055012538 TPR motif; other site 316055012539 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 316055012540 binding surface 316055012541 TPR motif; other site 316055012542 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 316055012543 binding surface 316055012544 TPR motif; other site 316055012545 TPR repeat; Region: TPR_11; pfam13414 316055012546 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 316055012547 binding surface 316055012548 TPR motif; other site 316055012549 TPR repeat; Region: TPR_11; pfam13414 316055012550 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 316055012551 hydroxyglutarate oxidase; Provisional; Region: PRK11728 316055012552 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 316055012553 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 316055012554 Fe-S cluster binding site [ion binding]; other site 316055012555 active site 316055012556 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 316055012557 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 316055012558 RNA/DNA hybrid binding site [nucleotide binding]; other site 316055012559 active site 316055012560 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 316055012561 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 316055012562 FeS/SAM binding site; other site 316055012563 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316055012564 MarR family; Region: MarR_2; pfam12802 316055012565 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 316055012566 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316055012567 Coenzyme A binding pocket [chemical binding]; other site 316055012568 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 316055012569 MPT binding site; other site 316055012570 trimer interface [polypeptide binding]; other site 316055012571 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 316055012572 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 316055012573 DNA methylase; Region: N6_N4_Mtase; pfam01555 316055012574 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 316055012575 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316055012576 minor groove reading motif; other site 316055012577 helix-hairpin-helix signature motif; other site 316055012578 substrate binding pocket [chemical binding]; other site 316055012579 active site 316055012580 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 316055012581 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 316055012582 DNA binding and oxoG recognition site [nucleotide binding] 316055012583 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 316055012584 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 316055012585 non-specific DNA binding site [nucleotide binding]; other site 316055012586 salt bridge; other site 316055012587 sequence-specific DNA binding site [nucleotide binding]; other site 316055012588 Protein of unknown function (DUF721); Region: DUF721; cl02324 316055012589 Thioredoxin; Region: Thioredoxin_4; pfam13462 316055012590 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 316055012591 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 316055012592 Peptidase family M48; Region: Peptidase_M48; cl12018 316055012593 Peptidase family M48; Region: Peptidase_M48; cl12018 316055012594 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 316055012595 Mitochondrial small ribosomal subunit Rsm22; Region: Rsm22; cl17847 316055012596 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 316055012597 AAA domain; Region: AAA_23; pfam13476 316055012598 Walker A/P-loop; other site 316055012599 ATP binding site [chemical binding]; other site 316055012600 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 316055012601 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 316055012602 ABC transporter signature motif; other site 316055012603 Walker B; other site 316055012604 D-loop; other site 316055012605 H-loop/switch region; other site 316055012606 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 316055012607 anthranilate synthase; Provisional; Region: PRK13566 316055012608 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 316055012609 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 316055012610 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 316055012611 glutamine binding [chemical binding]; other site 316055012612 catalytic triad [active] 316055012613 Protein of unknown function DUF86; Region: DUF86; cl01031 316055012614 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 316055012615 Methyltransferase domain; Region: Methyltransf_23; pfam13489 316055012616 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 316055012617 S-adenosylmethionine binding site [chemical binding]; other site 316055012618 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 316055012619 ABC1 family; Region: ABC1; pfam03109 316055012620 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 316055012621 PhnA protein; Region: PhnA; pfam03831 316055012622 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 316055012623 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 316055012624 acyl-activating enzyme (AAE) consensus motif; other site 316055012625 putative AMP binding site [chemical binding]; other site 316055012626 putative active site [active] 316055012627 putative CoA binding site [chemical binding]; other site 316055012628 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 316055012629 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055012630 classical (c) SDRs; Region: SDR_c; cd05233 316055012631 NAD(P) binding site [chemical binding]; other site 316055012632 active site 316055012633 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 316055012634 Radical SAM superfamily; Region: Radical_SAM; pfam04055 316055012635 FeS/SAM binding site; other site 316055012636 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 316055012637 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 316055012638 DctM-like transporters; Region: DctM; pfam06808 316055012639 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 316055012640 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 316055012641 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 316055012642 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 316055012643 active site 316055012644 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 316055012645 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 316055012646 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization...; Region: SQCY_1; cd02892 316055012647 Active site cavity [active] 316055012648 catalytic acid [active] 316055012649 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 316055012650 putative active site [active] 316055012651 putative CoA binding site [chemical binding]; other site 316055012652 nudix motif; other site 316055012653 metal binding site [ion binding]; metal-binding site 316055012654 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 316055012655 CoenzymeA binding site [chemical binding]; other site 316055012656 subunit interaction site [polypeptide binding]; other site 316055012657 PHB binding site; other site 316055012658 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 316055012659 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 316055012660 non-specific DNA binding site [nucleotide binding]; other site 316055012661 salt bridge; other site 316055012662 sequence-specific DNA binding site [nucleotide binding]; other site 316055012663 HipA N-terminal domain; Region: Couple_hipA; pfam13657 316055012664 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 316055012665 HipA-like N-terminal domain; Region: HipA_N; pfam07805 316055012666 HipA-like C-terminal domain; Region: HipA_C; pfam07804 316055012667 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 316055012668 non-specific DNA binding site [nucleotide binding]; other site 316055012669 salt bridge; other site 316055012670 sequence-specific DNA binding site [nucleotide binding]; other site 316055012671 zinc-binding protein; Provisional; Region: PRK01343 316055012672 Maf-like protein; Region: Maf; pfam02545 316055012673 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 316055012674 active site 316055012675 dimer interface [polypeptide binding]; other site 316055012676 Predicted ATPase [General function prediction only]; Region: COG4637 316055012677 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055012678 Walker A/P-loop; other site 316055012679 ATP binding site [chemical binding]; other site 316055012680 Low molecular weight phosphatase family; Region: LMWPc; cd00115 316055012681 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 316055012682 active site 316055012683 hypothetical protein; Provisional; Region: PRK02853 316055012684 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 316055012685 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 316055012686 NAD binding site [chemical binding]; other site 316055012687 dimerization interface [polypeptide binding]; other site 316055012688 product binding site; other site 316055012689 substrate binding site [chemical binding]; other site 316055012690 zinc binding site [ion binding]; other site 316055012691 catalytic residues [active] 316055012692 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 316055012693 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 316055012694 Protein of unknown function (DUF2948); Region: DUF2948; pfam11164 316055012695 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 316055012696 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 316055012697 hinge; other site 316055012698 active site 316055012699 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316055012700 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 316055012701 NAD(P) binding site [chemical binding]; other site 316055012702 active site 316055012703 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055012704 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055012705 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 316055012706 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 316055012707 EthD domain; Region: EthD; cl17553 316055012708 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055012709 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 316055012710 ligand binding site [chemical binding]; other site 316055012711 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 316055012712 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 316055012713 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 316055012714 SnoaL-like domain; Region: SnoaL_2; pfam12680 316055012715 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055012716 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055012717 DNA binding residues [nucleotide binding] 316055012718 dimerization interface [polypeptide binding]; other site 316055012719 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 316055012720 nudix motif; other site 316055012721 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055012722 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055012723 DNA binding residues [nucleotide binding] 316055012724 dimerization interface [polypeptide binding]; other site 316055012725 Flagellar protein FlbT; Region: FlbT; cl11455 316055012726 flagellin; Provisional; Region: PRK14708 316055012727 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316055012728 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055012729 Domain of Unknown Function (DUF1522); Region: DUF1522; pfam07482 316055012730 GTPase RsgA; Reviewed; Region: PRK01889 316055012731 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 316055012732 RNA binding site [nucleotide binding]; other site 316055012733 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 316055012734 GTPase/Zn-binding domain interface [polypeptide binding]; other site 316055012735 GTP/Mg2+ binding site [chemical binding]; other site 316055012736 G4 box; other site 316055012737 G5 box; other site 316055012738 G1 box; other site 316055012739 Switch I region; other site 316055012740 G2 box; other site 316055012741 G3 box; other site 316055012742 Switch II region; other site 316055012743 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 316055012744 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 316055012745 Predicted protein-tyrosine phosphatase [Signal transduction mechanisms]; Region: CDC14; COG2453 316055012746 active site 316055012747 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 316055012748 HipA-like N-terminal domain; Region: HipA_N; pfam07805 316055012749 Protein of unknown function (DUF3419); Region: DUF3419; pfam11899 316055012750 Methyltransferase domain; Region: Methyltransf_31; pfam13847 316055012751 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 316055012752 S-adenosylmethionine binding site [chemical binding]; other site 316055012753 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 316055012754 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 316055012755 Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily; Region: ZntB_u1; cd12834 316055012756 Cl binding site [ion binding]; other site 316055012757 oligomer interface [polypeptide binding]; other site 316055012758 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 316055012759 active site 316055012760 Ap6A binding site [chemical binding]; other site 316055012761 nudix motif; other site 316055012762 metal binding site [ion binding]; metal-binding site 316055012763 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 316055012764 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 316055012765 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 316055012766 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 316055012767 dimer interface [polypeptide binding]; other site 316055012768 decamer (pentamer of dimers) interface [polypeptide binding]; other site 316055012769 catalytic triad [active] 316055012770 peroxidatic and resolving cysteines [active] 316055012771 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 316055012772 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 316055012773 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 316055012774 oxidoreductase; Provisional; Region: PRK10015 316055012775 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 316055012776 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 316055012777 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 316055012778 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 316055012779 Ligand binding site [chemical binding]; other site 316055012780 Electron transfer flavoprotein domain; Region: ETF; pfam01012 316055012781 nitrogenase stabilizing/protective protein; Provisional; Region: nifW; PRK00810 316055012782 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 316055012783 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 316055012784 active site 316055012785 catalytic residues [active] 316055012786 metal binding site [ion binding]; metal-binding site 316055012787 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 316055012788 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 316055012789 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055012790 catalytic residue [active] 316055012791 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 316055012792 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 316055012793 trimerization site [polypeptide binding]; other site 316055012794 active site 316055012795 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 316055012796 NifU-like domain; Region: NifU; pfam01106 316055012797 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 316055012798 NifQ; Region: NifQ; pfam04891 316055012799 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 316055012800 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 316055012801 Rop-like; Region: Rop-like; pfam05082 316055012802 probable nitrogen fixation protein; Region: TIGR02935 316055012803 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 316055012804 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 316055012805 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 316055012806 nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional; Region: PRK14478 316055012807 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 316055012808 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 316055012809 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 316055012810 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 316055012811 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 316055012812 MoFe protein beta/alpha subunit interactions; other site 316055012813 Beta subunit P cluster binding residues; other site 316055012814 MoFe protein beta subunit/Fe protein contacts; other site 316055012815 MoFe protein dimer/ dimer interactions; other site 316055012816 Nitrogenase molybdenum-iron protein, alpha and beta chains [Energy production and conversion]; Region: NifD; COG2710 316055012817 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 316055012818 MoFe protein alpha/beta subunit interactions; other site 316055012819 Alpha subunit P cluster binding residues; other site 316055012820 FeMoco binding residues [chemical binding]; other site 316055012821 MoFe protein alpha subunit/Fe protein contacts; other site 316055012822 MoFe protein dimer/ dimer interactions; other site 316055012823 nitrogenase reductase; Reviewed; Region: nifH; PRK13234 316055012824 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 316055012825 Nucleotide-binding sites [chemical binding]; other site 316055012826 Walker A motif; other site 316055012827 Switch I region of nucleotide binding site; other site 316055012828 Fe4S4 binding sites [ion binding]; other site 316055012829 Switch II region of nucleotide binding site; other site 316055012830 SIR2-like domain; Region: SIR2_2; pfam13289 316055012831 NifT/FixU protein; Region: NifT; pfam06988 316055012832 NifZ domain; Region: NifZ; pfam04319 316055012833 NifZ domain; Region: NifZ; pfam04319 316055012834 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 316055012835 archaeoflavoprotein, MJ0208 family; Region: flavo_MJ0208; TIGR02700 316055012836 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 316055012837 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 316055012838 FeS/SAM binding site; other site 316055012839 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 316055012840 hypothetical protein; Provisional; Region: PRK13795 316055012841 Nif-specific regulatory protein; Region: nifA; TIGR01817 316055012842 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 316055012843 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055012844 Walker A motif; other site 316055012845 ATP binding site [chemical binding]; other site 316055012846 Walker B motif; other site 316055012847 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 316055012848 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055012849 classical (c) SDRs; Region: SDR_c; cd05233 316055012850 NAD(P) binding site [chemical binding]; other site 316055012851 active site 316055012852 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 316055012853 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 316055012854 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 316055012855 dimer interface [polypeptide binding]; other site 316055012856 acyl-activating enzyme (AAE) consensus motif; other site 316055012857 putative active site [active] 316055012858 AMP binding site [chemical binding]; other site 316055012859 putative CoA binding site [chemical binding]; other site 316055012860 Antenna complex alpha/beta subunit; Region: LHC; pfam00556 316055012861 HAMP domain; Region: HAMP; pfam00672 316055012862 dimerization interface [polypeptide binding]; other site 316055012863 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 316055012864 cyclase homology domain; Region: CHD; cd07302 316055012865 nucleotidyl binding site; other site 316055012866 metal binding site [ion binding]; metal-binding site 316055012867 dimer interface [polypeptide binding]; other site 316055012868 Protein of unknown function (DUF3175); Region: DUF3175; pfam11373 316055012869 phosphoglycerate transporter family protein; Region: 2A0104; TIGR00881 316055012870 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 316055012871 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 316055012872 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 316055012873 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 316055012874 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 316055012875 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 316055012876 active site 316055012877 homotetramer interface [polypeptide binding]; other site 316055012878 haemagglutination activity domain; Region: Haemagg_act; smart00912 316055012879 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 316055012880 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 316055012881 FecR protein; Region: FecR; pfam04773 316055012882 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 316055012883 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055012884 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 316055012885 Secretin and TonB N terminus short domain; Region: STN; smart00965 316055012886 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316055012887 Uncharacterized protein conserved in archaea [Function unknown]; Region: COG3398 316055012888 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 316055012889 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 316055012890 Ca2+ binding site [ion binding]; other site 316055012891 EF-hand domain pair; Region: EF_hand_5; pfam13499 316055012892 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 316055012893 Ca2+ binding site [ion binding]; other site 316055012894 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055012895 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 316055012896 active site 316055012897 phosphorylation site [posttranslational modification] 316055012898 intermolecular recognition site; other site 316055012899 dimerization interface [polypeptide binding]; other site 316055012900 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055012901 DNA binding site [nucleotide binding] 316055012902 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055012903 dimer interface [polypeptide binding]; other site 316055012904 phosphorylation site [posttranslational modification] 316055012905 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 316055012906 ATP binding site [chemical binding]; other site 316055012907 Mg2+ binding site [ion binding]; other site 316055012908 G-X-G motif; other site 316055012909 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 316055012910 EamA-like transporter family; Region: EamA; pfam00892 316055012911 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 316055012912 dimerization interface [polypeptide binding]; other site 316055012913 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055012914 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055012915 dimer interface [polypeptide binding]; other site 316055012916 putative CheW interface [polypeptide binding]; other site 316055012917 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 316055012918 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 316055012919 catalytic loop [active] 316055012920 iron binding site [ion binding]; other site 316055012921 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 316055012922 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316055012923 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316055012924 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 316055012925 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316055012926 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 316055012927 FAD binding domain; Region: FAD_binding_4; pfam01565 316055012928 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 316055012929 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055012930 putative CheW interface [polypeptide binding]; other site 316055012931 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 316055012932 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 316055012933 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 316055012934 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 316055012935 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 316055012936 ApbE family; Region: ApbE; pfam02424 316055012937 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 316055012938 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 316055012939 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 316055012940 N-terminal plug; other site 316055012941 ligand-binding site [chemical binding]; other site 316055012942 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316055012943 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 316055012944 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 316055012945 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 316055012946 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 316055012947 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 316055012948 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 316055012949 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 316055012950 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316055012951 Protein of unknown function (DUF3616); Region: DUF3616; pfam12275 316055012952 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 316055012953 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_3; cd05971 316055012954 active site 316055012955 acyl-activating enzyme (AAE) consensus motif; other site 316055012956 putative CoA binding site [chemical binding]; other site 316055012957 AMP binding site [chemical binding]; other site 316055012958 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 316055012959 Transposase domain (DUF772); Region: DUF772; pfam05598 316055012960 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 316055012961 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 316055012962 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 316055012963 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 316055012964 Tetramer interface [polypeptide binding]; other site 316055012965 active site 316055012966 FMN-binding site [chemical binding]; other site 316055012967 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 316055012968 catalytic core [active] 316055012969 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 316055012970 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 316055012971 NAD binding site [chemical binding]; other site 316055012972 homotetramer interface [polypeptide binding]; other site 316055012973 homodimer interface [polypeptide binding]; other site 316055012974 substrate binding site [chemical binding]; other site 316055012975 active site 316055012976 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 316055012977 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 316055012978 HSP70 interaction site [polypeptide binding]; other site 316055012979 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 316055012980 substrate binding site [polypeptide binding]; other site 316055012981 dimer interface [polypeptide binding]; other site 316055012982 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 316055012983 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 316055012984 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 316055012985 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 316055012986 classical (c) SDRs; Region: SDR_c; cd05233 316055012987 NAD(P) binding site [chemical binding]; other site 316055012988 active site 316055012989 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 316055012990 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 316055012991 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 316055012992 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 316055012993 Walker A/P-loop; other site 316055012994 ATP binding site [chemical binding]; other site 316055012995 Q-loop/lid; other site 316055012996 ABC transporter signature motif; other site 316055012997 Walker B; other site 316055012998 D-loop; other site 316055012999 H-loop/switch region; other site 316055013000 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 316055013001 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 316055013002 Walker A/P-loop; other site 316055013003 ATP binding site [chemical binding]; other site 316055013004 Q-loop/lid; other site 316055013005 ABC transporter signature motif; other site 316055013006 Walker B; other site 316055013007 D-loop; other site 316055013008 H-loop/switch region; other site 316055013009 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055013010 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 316055013011 TM-ABC transporter signature motif; other site 316055013012 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 316055013013 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 316055013014 TM-ABC transporter signature motif; other site 316055013015 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 316055013016 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 316055013017 putative ligand binding site [chemical binding]; other site 316055013018 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 316055013019 Na binding site [ion binding]; other site 316055013020 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055013021 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013022 dimer interface [polypeptide binding]; other site 316055013023 phosphorylation site [posttranslational modification] 316055013024 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 316055013025 ATP binding site [chemical binding]; other site 316055013026 Mg2+ binding site [ion binding]; other site 316055013027 G-X-G motif; other site 316055013028 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055013029 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 316055013030 active site 316055013031 phosphorylation site [posttranslational modification] 316055013032 intermolecular recognition site; other site 316055013033 dimerization interface [polypeptide binding]; other site 316055013034 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 316055013035 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 316055013036 Response regulator receiver domain; Region: Response_reg; pfam00072 316055013037 active site 316055013038 phosphorylation site [posttranslational modification] 316055013039 intermolecular recognition site; other site 316055013040 dimerization interface [polypeptide binding]; other site 316055013041 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055013042 DNA binding residues [nucleotide binding] 316055013043 Protein of unknown function (DUF1469); Region: DUF1469; pfam07332 316055013044 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 316055013045 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 316055013046 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055013047 acyl-activating enzyme (AAE) consensus motif; other site 316055013048 acyl-activating enzyme (AAE) consensus motif; other site 316055013049 putative AMP binding site [chemical binding]; other site 316055013050 putative active site [active] 316055013051 putative CoA binding site [chemical binding]; other site 316055013052 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055013053 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 316055013054 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 316055013055 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 316055013056 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 316055013057 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 316055013058 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 316055013059 Ligand-binding SRPBCC domain of Micromonospora echinospora CalC and related proteins; Region: SRPBCC_CalC; cd08891 316055013060 putative hydrophobic ligand binding site [chemical binding]; other site 316055013061 CLM binding site; other site 316055013062 L1 loop; other site 316055013063 DNA binding site [nucleotide binding] 316055013064 Winged helix DNA-binding domain; Region: HTH_34; pfam13601 316055013065 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 316055013066 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 316055013067 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 316055013068 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 316055013069 generic binding surface II; other site 316055013070 generic binding surface I; other site 316055013071 Glucokinase; Region: Glucokinase; pfam02685 316055013072 glucokinase, proteobacterial type; Region: glk; TIGR00749 316055013073 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 316055013074 beta-galactosidase; Region: BGL; TIGR03356 316055013075 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316055013076 Beta-lactamase; Region: Beta-lactamase; pfam00144 316055013077 hypothetical protein; Provisional; Region: PRK11770 316055013078 Domain of unknown function (DUF307); Region: DUF307; pfam03733 316055013079 Domain of unknown function (DUF307); Region: DUF307; pfam03733 316055013080 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 316055013081 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 316055013082 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316055013083 Soluble P-type ATPase [General function prediction only]; Region: COG4087 316055013084 potassium-transporting ATPase subunit C; Provisional; Region: PRK13999 316055013085 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 316055013086 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 316055013087 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 316055013088 Ligand Binding Site [chemical binding]; other site 316055013089 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 316055013090 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013091 dimer interface [polypeptide binding]; other site 316055013092 phosphorylation site [posttranslational modification] 316055013093 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 316055013094 ATP binding site [chemical binding]; other site 316055013095 Mg2+ binding site [ion binding]; other site 316055013096 G-X-G motif; other site 316055013097 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055013098 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 316055013099 active site 316055013100 phosphorylation site [posttranslational modification] 316055013101 intermolecular recognition site; other site 316055013102 dimerization interface [polypeptide binding]; other site 316055013103 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055013104 DNA binding site [nucleotide binding] 316055013105 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 316055013106 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 316055013107 ligand binding site [chemical binding]; other site 316055013108 flexible hinge region; other site 316055013109 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 316055013110 putative switch regulator; other site 316055013111 non-specific DNA interactions [nucleotide binding]; other site 316055013112 DNA binding site [nucleotide binding] 316055013113 sequence specific DNA binding site [nucleotide binding]; other site 316055013114 putative cAMP binding site [chemical binding]; other site 316055013115 cyclase homology domain; Region: CHD; cd07302 316055013116 nucleotidyl binding site; other site 316055013117 metal binding site [ion binding]; metal-binding site 316055013118 dimer interface [polypeptide binding]; other site 316055013119 AAA ATPase domain; Region: AAA_16; pfam13191 316055013120 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 316055013121 TPR motif; other site 316055013122 binding surface 316055013123 Tetratricopeptide repeat; Region: TPR_12; pfam13424 316055013124 Cytochrome P450; Region: p450; cl12078 316055013125 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 316055013126 Haemolysin-III related; Region: HlyIII; cl03831 316055013127 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 316055013128 cyanate hydratase; Validated; Region: PRK02866 316055013129 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 316055013130 oligomer interface [polypeptide binding]; other site 316055013131 active site 316055013132 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 316055013133 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 316055013134 Walker A/P-loop; other site 316055013135 ATP binding site [chemical binding]; other site 316055013136 Q-loop/lid; other site 316055013137 ABC transporter signature motif; other site 316055013138 Walker B; other site 316055013139 D-loop; other site 316055013140 H-loop/switch region; other site 316055013141 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 316055013142 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055013143 dimer interface [polypeptide binding]; other site 316055013144 conserved gate region; other site 316055013145 putative PBP binding loops; other site 316055013146 ABC-ATPase subunit interface; other site 316055013147 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316055013148 NMT1-like family; Region: NMT1_2; pfam13379 316055013149 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 316055013150 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 316055013151 putative active site [active] 316055013152 heme pocket [chemical binding]; other site 316055013153 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 316055013154 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055013155 Walker A motif; other site 316055013156 ATP binding site [chemical binding]; other site 316055013157 Walker B motif; other site 316055013158 arginine finger; other site 316055013159 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055013160 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 316055013161 active site 316055013162 catalytic residues [active] 316055013163 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055013164 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 316055013165 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cd00138 316055013166 putative active site [active] 316055013167 catalytic site [active] 316055013168 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Region: PLDc_unchar1_2; cd09128 316055013169 PLD-like domain; Region: PLDc_2; pfam13091 316055013170 putative active site [active] 316055013171 putative catalytic site [active] 316055013172 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316055013173 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 316055013174 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 316055013175 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 316055013176 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 316055013177 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 316055013178 catalytic loop [active] 316055013179 iron binding site [ion binding]; other site 316055013180 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 316055013181 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 316055013182 [4Fe-4S] binding site [ion binding]; other site 316055013183 molybdopterin cofactor binding site; other site 316055013184 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 316055013185 molybdopterin cofactor binding site; other site 316055013186 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 316055013187 putative dimer interface [polypeptide binding]; other site 316055013188 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 316055013189 SLBB domain; Region: SLBB; pfam10531 316055013190 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 316055013191 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 316055013192 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 316055013193 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316055013194 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 316055013195 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 316055013196 dimerization interface [polypeptide binding]; other site 316055013197 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 316055013198 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055013199 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055013200 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 316055013201 CHAD domain; Region: CHAD; pfam05235 316055013202 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013203 dimer interface [polypeptide binding]; other site 316055013204 phosphorylation site [posttranslational modification] 316055013205 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 316055013206 ATP binding site [chemical binding]; other site 316055013207 Mg2+ binding site [ion binding]; other site 316055013208 G-X-G motif; other site 316055013209 osmolarity response regulator; Provisional; Region: ompR; PRK09468 316055013210 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 316055013211 active site 316055013212 phosphorylation site [posttranslational modification] 316055013213 intermolecular recognition site; other site 316055013214 dimerization interface [polypeptide binding]; other site 316055013215 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055013216 DNA binding site [nucleotide binding] 316055013217 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 316055013218 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 316055013219 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316055013220 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055013221 YtkA-like; Region: YtkA; pfam13115 316055013222 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055013223 dimer interface [polypeptide binding]; other site 316055013224 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 316055013225 putative CheW interface [polypeptide binding]; other site 316055013226 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 316055013227 PAS fold; Region: PAS_3; pfam08447 316055013228 putative active site [active] 316055013229 heme pocket [chemical binding]; other site 316055013230 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316055013231 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 316055013232 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 316055013233 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055013234 Walker A/P-loop; other site 316055013235 ATP binding site [chemical binding]; other site 316055013236 Q-loop/lid; other site 316055013237 ABC transporter signature motif; other site 316055013238 Walker B; other site 316055013239 D-loop; other site 316055013240 H-loop/switch region; other site 316055013241 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 316055013242 Walker A/P-loop; other site 316055013243 ATP binding site [chemical binding]; other site 316055013244 Q-loop/lid; other site 316055013245 ABC transporter signature motif; other site 316055013246 Walker B; other site 316055013247 D-loop; other site 316055013248 H-loop/switch region; other site 316055013249 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316055013250 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 316055013251 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 316055013252 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 316055013253 HlyD family secretion protein; Region: HlyD_3; pfam13437 316055013254 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055013255 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055013256 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 316055013257 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 316055013258 active site 316055013259 phosphorylation site [posttranslational modification] 316055013260 intermolecular recognition site; other site 316055013261 dimerization interface [polypeptide binding]; other site 316055013262 CheB methylesterase; Region: CheB_methylest; pfam01339 316055013263 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316055013264 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 316055013265 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 316055013266 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 316055013267 putative CheA interaction surface; other site 316055013268 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055013269 dimerization interface [polypeptide binding]; other site 316055013270 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055013271 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055013272 dimer interface [polypeptide binding]; other site 316055013273 putative CheW interface [polypeptide binding]; other site 316055013274 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 316055013275 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 316055013276 dimerization interface [polypeptide binding]; other site 316055013277 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055013278 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055013279 dimer interface [polypeptide binding]; other site 316055013280 putative CheW interface [polypeptide binding]; other site 316055013281 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 316055013282 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 316055013283 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 316055013284 putative binding surface; other site 316055013285 active site 316055013286 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316055013287 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 316055013288 ATP binding site [chemical binding]; other site 316055013289 Mg2+ binding site [ion binding]; other site 316055013290 G-X-G motif; other site 316055013291 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 316055013292 Response regulator receiver domain; Region: Response_reg; pfam00072 316055013293 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 316055013294 active site 316055013295 phosphorylation site [posttranslational modification] 316055013296 intermolecular recognition site; other site 316055013297 dimerization interface [polypeptide binding]; other site 316055013298 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 316055013299 anti sigma factor interaction site; other site 316055013300 regulatory phosphorylation site [posttranslational modification]; other site 316055013301 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 316055013302 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 316055013303 substrate binding site [chemical binding]; other site 316055013304 catalytic Zn binding site [ion binding]; other site 316055013305 NAD binding site [chemical binding]; other site 316055013306 structural Zn binding site [ion binding]; other site 316055013307 dimer interface [polypeptide binding]; other site 316055013308 glutathione-dependent formaldehyde-activating enzyme; Provisional; Region: PRK05417 316055013309 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 316055013310 S-formylglutathione hydrolase; Region: PLN02442 316055013311 Protein of unknown function (DUF2380); Region: DUF3280; pfam11684 316055013312 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316055013313 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 316055013314 ligand binding site [chemical binding]; other site 316055013315 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 316055013316 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 316055013317 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 316055013318 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 316055013319 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 316055013320 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 316055013321 Walker A/P-loop; other site 316055013322 ATP binding site [chemical binding]; other site 316055013323 Q-loop/lid; other site 316055013324 ABC transporter signature motif; other site 316055013325 Walker B; other site 316055013326 D-loop; other site 316055013327 H-loop/switch region; other site 316055013328 ABC-2 type transporter; Region: ABC2_membrane; cl17235 316055013329 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316055013330 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 316055013331 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 316055013332 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 316055013333 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 316055013334 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 316055013335 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 316055013336 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 316055013337 Cysteine-rich domain; Region: CCG; pfam02754 316055013338 Cysteine-rich domain; Region: CCG; pfam02754 316055013339 FAD binding domain; Region: FAD_binding_4; pfam01565 316055013340 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 316055013341 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 316055013342 FAD binding domain; Region: FAD_binding_4; pfam01565 316055013343 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055013344 Predicted membrane protein [Function unknown]; Region: COG4541 316055013345 AzlC protein; Region: AzlC; cl00570 316055013346 FtsH Extracellular; Region: FtsH_ext; pfam06480 316055013347 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 316055013348 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055013349 Walker A motif; other site 316055013350 ATP binding site [chemical binding]; other site 316055013351 Walker B motif; other site 316055013352 arginine finger; other site 316055013353 Peptidase family M41; Region: Peptidase_M41; pfam01434 316055013354 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 316055013355 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 316055013356 Ligand Binding Site [chemical binding]; other site 316055013357 basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Region: B_zip1; cl02576 316055013358 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 316055013359 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055013360 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055013361 ligand binding site [chemical binding]; other site 316055013362 Cupin domain; Region: Cupin_2; cl17218 316055013363 Helix-turn-helix domain; Region: HTH_18; pfam12833 316055013364 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316055013365 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 316055013366 S-adenosylmethionine binding site [chemical binding]; other site 316055013367 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 316055013368 PAS fold; Region: PAS_7; pfam12860 316055013369 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055013370 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055013371 metal binding site [ion binding]; metal-binding site 316055013372 active site 316055013373 I-site; other site 316055013374 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 316055013375 translocation protein TolB; Provisional; Region: tolB; PRK05137 316055013376 TolB amino-terminal domain; Region: TolB_N; pfam04052 316055013377 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316055013378 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316055013379 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316055013380 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316055013381 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 316055013382 TolR protein; Region: tolR; TIGR02801 316055013383 TolQ protein; Region: tolQ; TIGR02796 316055013384 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 316055013385 Protein of unknown function (DUF2852); Region: DUF2852; pfam11014 316055013386 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316055013387 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316055013388 WHG domain; Region: WHG; pfam13305 316055013389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 316055013390 Ketosteroid isomerase-related protein [General function prediction only]; Region: COG3631 316055013391 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316055013392 classical (c) SDRs; Region: SDR_c; cd05233 316055013393 NAD(P) binding site [chemical binding]; other site 316055013394 active site 316055013395 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 316055013396 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 316055013397 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 316055013398 active site 316055013399 dimerization interface [polypeptide binding]; other site 316055013400 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316055013401 Sel1-like repeats; Region: SEL1; smart00671 316055013402 Sel1-like repeats; Region: SEL1; smart00671 316055013403 Sel1-like repeats; Region: SEL1; smart00671 316055013404 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 316055013405 thiamine phosphate binding site [chemical binding]; other site 316055013406 active site 316055013407 pyrophosphate binding site [ion binding]; other site 316055013408 Class I aldolases; Region: Aldolase_Class_I; cl17187 316055013409 catalytic residue [active] 316055013410 PemK-like protein; Region: PemK; pfam02452 316055013411 Protein of unknown function (DUF3018); Region: DUF3018; pfam11455 316055013412 Phosphoglycerate kinase; Region: PGK; pfam00162 316055013413 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; cd00318 316055013414 substrate binding site [chemical binding]; other site 316055013415 hinge regions; other site 316055013416 ADP binding site [chemical binding]; other site 316055013417 catalytic site [active] 316055013418 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 316055013419 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 316055013420 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 316055013421 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 316055013422 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 316055013423 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 316055013424 TPP-binding site [chemical binding]; other site 316055013425 dimer interface [polypeptide binding]; other site 316055013426 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 316055013427 PYR/PP interface [polypeptide binding]; other site 316055013428 dimer interface [polypeptide binding]; other site 316055013429 TPP binding site [chemical binding]; other site 316055013430 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316055013431 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 316055013432 Cell division protein ZapA; Region: ZapA; pfam05164 316055013433 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 316055013434 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 316055013435 PAS domain; Region: PAS_9; pfam13426 316055013436 putative active site [active] 316055013437 heme pocket [chemical binding]; other site 316055013438 PAS domain S-box; Region: sensory_box; TIGR00229 316055013439 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 316055013440 putative active site [active] 316055013441 heme pocket [chemical binding]; other site 316055013442 PAS domain; Region: PAS; smart00091 316055013443 PAS fold; Region: PAS_7; pfam12860 316055013444 PAS fold; Region: PAS_7; pfam12860 316055013445 PAS fold; Region: PAS_7; pfam12860 316055013446 PAS fold; Region: PAS_7; pfam12860 316055013447 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 316055013448 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316055013449 metal binding site [ion binding]; metal-binding site 316055013450 active site 316055013451 I-site; other site 316055013452 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 316055013453 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 316055013454 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 316055013455 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316055013456 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 316055013457 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 316055013458 dimer interface [polypeptide binding]; other site 316055013459 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 316055013460 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 316055013461 putative substrate translocation pore; other site 316055013462 putative protease; Provisional; Region: PRK15447 316055013463 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 316055013464 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 316055013465 Peptidase family U32; Region: Peptidase_U32; pfam01136 316055013466 SCP-2 sterol transfer family; Region: SCP2; cl01225 316055013467 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 316055013468 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 316055013469 Flavoprotein; Region: Flavoprotein; pfam02441 316055013470 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 316055013471 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 316055013472 salt bridge; other site 316055013473 non-specific DNA binding site [nucleotide binding]; other site 316055013474 sequence-specific DNA binding site [nucleotide binding]; other site 316055013475 protease TldD; Provisional; Region: tldD; PRK10735 316055013476 Protein of unknown function (DUF433); Region: DUF433; pfam04255 316055013477 Predicted membrane protein [Function unknown]; Region: COG4325 316055013478 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 316055013479 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 316055013480 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 316055013481 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 316055013482 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 316055013483 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 316055013484 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 316055013485 Subunit I/III interface [polypeptide binding]; other site 316055013486 D-pathway; other site 316055013487 Subunit I/VIIc interface [polypeptide binding]; other site 316055013488 Subunit I/IV interface [polypeptide binding]; other site 316055013489 Subunit I/II interface [polypeptide binding]; other site 316055013490 Low-spin heme (heme a) binding site [chemical binding]; other site 316055013491 Subunit I/VIIa interface [polypeptide binding]; other site 316055013492 Subunit I/VIa interface [polypeptide binding]; other site 316055013493 Dimer interface; other site 316055013494 Putative water exit pathway; other site 316055013495 Binuclear center (heme a3/CuB) [ion binding]; other site 316055013496 K-pathway; other site 316055013497 Subunit I/Vb interface [polypeptide binding]; other site 316055013498 Putative proton exit pathway; other site 316055013499 Subunit I/VIb interface; other site 316055013500 Subunit I/VIc interface [polypeptide binding]; other site 316055013501 Electron transfer pathway; other site 316055013502 Subunit I/VIIIb interface [polypeptide binding]; other site 316055013503 Subunit I/VIIb interface [polypeptide binding]; other site 316055013504 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 316055013505 UbiA prenyltransferase family; Region: UbiA; pfam01040 316055013506 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 316055013507 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 316055013508 Subunit III/VIIa interface [polypeptide binding]; other site 316055013509 Phospholipid binding site [chemical binding]; other site 316055013510 Subunit I/III interface [polypeptide binding]; other site 316055013511 Subunit III/VIb interface [polypeptide binding]; other site 316055013512 Subunit III/VIa interface; other site 316055013513 Subunit III/Vb interface [polypeptide binding]; other site 316055013514 Protein of unknown function (DUF983); Region: DUF983; cl02211 316055013515 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 316055013516 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 316055013517 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 316055013518 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055013519 catalytic residue [active] 316055013520 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316055013521 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 316055013522 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316055013523 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316055013524 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 316055013525 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 316055013526 active site 316055013527 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 316055013528 Uncharacterized protein conserved in bacteria (DUF2191); Region: DUF2191; pfam09957 316055013529 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 316055013530 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055013531 Walker A motif; other site 316055013532 ATP binding site [chemical binding]; other site 316055013533 Walker B motif; other site 316055013534 arginine finger; other site 316055013535 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 316055013536 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 316055013537 active site 316055013538 catalytic motif [active] 316055013539 Zn binding site [ion binding]; other site 316055013540 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 316055013541 RuvA N terminal domain; Region: RuvA_N; pfam01330 316055013542 Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase; cl00205 316055013543 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 316055013544 active site 316055013545 putative DNA-binding cleft [nucleotide binding]; other site 316055013546 dimer interface [polypeptide binding]; other site 316055013547 hypothetical protein; Validated; Region: PRK00110 316055013548 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316055013549 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 316055013550 dimer interface [polypeptide binding]; other site 316055013551 putative CheW interface [polypeptide binding]; other site 316055013552 B12-binding domain/radical SAM domain protein, MJ_1487 family; Region: B12_SAM_MJ_1487; TIGR04013 316055013553 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 316055013554 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 316055013555 FeS/SAM binding site; other site 316055013556 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 316055013557 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316055013558 putative active site [active] 316055013559 metal binding site [ion binding]; metal-binding site 316055013560 homodimer binding site [polypeptide binding]; other site 316055013561 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 316055013562 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 316055013563 F0F1 ATP synthase subunit B; Provisional; Region: PRK14475 316055013564 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 316055013565 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 316055013566 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 316055013567 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 316055013568 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 316055013569 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 316055013570 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 316055013571 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 316055013572 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 316055013573 putative catalytic residue [active] 316055013574 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 316055013575 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 316055013576 putative substrate translocation pore; other site 316055013577 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316055013578 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 316055013579 active site 316055013580 phosphorylation site [posttranslational modification] 316055013581 intermolecular recognition site; other site 316055013582 dimerization interface [polypeptide binding]; other site 316055013583 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 316055013584 DNA binding residues [nucleotide binding] 316055013585 dimerization interface [polypeptide binding]; other site 316055013586 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 316055013587 Na binding site [ion binding]; other site 316055013588 PAS fold; Region: PAS_7; pfam12860 316055013589 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055013590 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013591 dimer interface [polypeptide binding]; other site 316055013592 phosphorylation site [posttranslational modification] 316055013593 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 316055013594 ATP binding site [chemical binding]; other site 316055013595 Mg2+ binding site [ion binding]; other site 316055013596 G-X-G motif; other site 316055013597 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 316055013598 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 316055013599 active site 316055013600 phosphorylation site [posttranslational modification] 316055013601 intermolecular recognition site; other site 316055013602 dimerization interface [polypeptide binding]; other site 316055013603 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 316055013604 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 316055013605 substrate-cofactor binding pocket; other site 316055013606 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055013607 catalytic residue [active] 316055013608 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 316055013609 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 316055013610 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 316055013611 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 316055013612 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 316055013613 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 316055013614 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 316055013615 ABC-ATPase subunit interface; other site 316055013616 dimer interface [polypeptide binding]; other site 316055013617 putative PBP binding regions; other site 316055013618 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 316055013619 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 316055013620 metal binding site [ion binding]; metal-binding site 316055013621 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 316055013622 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 316055013623 P-loop, Walker A motif; other site 316055013624 Base recognition motif; other site 316055013625 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 316055013626 FOG: WD40 repeat [General function prediction only]; Region: COG2319 316055013627 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 316055013628 structural tetrad; other site 316055013629 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 316055013630 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 316055013631 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_6; cd06154 316055013632 homotrimer interaction site [polypeptide binding]; other site 316055013633 putative active site [active] 316055013634 Predicted acetyltransferase [General function prediction only]; Region: COG3153 316055013635 Coenzyme A binding pocket [chemical binding]; other site 316055013636 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 316055013637 dimer interface [polypeptide binding]; other site 316055013638 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 316055013639 active site 316055013640 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 316055013641 catalytic residues [active] 316055013642 substrate binding site [chemical binding]; other site 316055013643 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 316055013644 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 316055013645 active site 316055013646 Zn binding site [ion binding]; other site 316055013647 Protein of unknown function (DUF1007); Region: DUF1007; pfam06226 316055013648 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG2215 316055013649 ferrochelatase; Reviewed; Region: hemH; PRK00035 316055013650 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 316055013651 C-terminal domain interface [polypeptide binding]; other site 316055013652 active site 316055013653 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 316055013654 active site 316055013655 N-terminal domain interface [polypeptide binding]; other site 316055013656 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 316055013657 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 316055013658 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 316055013659 recombination protein RecR; Reviewed; Region: recR; PRK00076 316055013660 RecR protein; Region: RecR; pfam02132 316055013661 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 316055013662 tetramer interface [polypeptide binding]; other site 316055013663 putative active site [active] 316055013664 putative metal-binding site [ion binding]; other site 316055013665 hypothetical protein; Validated; Region: PRK00153 316055013666 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 316055013667 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 316055013668 Walker A motif; other site 316055013669 ATP binding site [chemical binding]; other site 316055013670 Walker B motif; other site 316055013671 arginine finger; other site 316055013672 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 316055013673 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 316055013674 HIT domain; Region: HIT; pfam01230 316055013675 nucleotide binding site/active site [active] 316055013676 HIT family signature motif; other site 316055013677 catalytic residue [active] 316055013678 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 316055013679 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 316055013680 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 316055013681 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 316055013682 putative NADH binding site [chemical binding]; other site 316055013683 putative active site [active] 316055013684 nudix motif; other site 316055013685 putative metal binding site [ion binding]; other site 316055013686 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 316055013687 Ribokinase-like subgroup B. Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_B; cd01945 316055013688 substrate binding site [chemical binding]; other site 316055013689 ATP binding site [chemical binding]; other site 316055013690 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 316055013691 catalytic motif [active] 316055013692 Catalytic residue [active] 316055013693 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 316055013694 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 316055013695 putative Mg++ binding site [ion binding]; other site 316055013696 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 316055013697 nucleotide binding region [chemical binding]; other site 316055013698 ATP-binding site [chemical binding]; other site 316055013699 Helicase associated domain (HA2); Region: HA2; cl04503 316055013700 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 316055013701 Predicted membrane protein [Function unknown]; Region: COG4763 316055013702 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055013703 5'-3' exonuclease; Region: 53EXOc; smart00475 316055013704 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 316055013705 active site 316055013706 metal binding site 1 [ion binding]; metal-binding site 316055013707 putative 5' ssDNA interaction site; other site 316055013708 metal binding site 3; metal-binding site 316055013709 metal binding site 2 [ion binding]; metal-binding site 316055013710 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 316055013711 putative DNA binding site [nucleotide binding]; other site 316055013712 putative metal binding site [ion binding]; other site 316055013713 DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]; Region: PolA; COG0749 316055013714 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 316055013715 active site 316055013716 catalytic site [active] 316055013717 substrate binding site [chemical binding]; other site 316055013718 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 316055013719 active site 316055013720 DNA binding site [nucleotide binding] 316055013721 catalytic site [active] 316055013722 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 316055013723 active site 316055013724 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 316055013725 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 316055013726 homodimer interface [polypeptide binding]; other site 316055013727 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 316055013728 active site pocket [active] 316055013729 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 316055013730 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 316055013731 putative active site pocket [active] 316055013732 dimerization interface [polypeptide binding]; other site 316055013733 putative catalytic residue [active] 316055013734 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 316055013735 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 316055013736 putative acyl-acceptor binding pocket; other site 316055013737 Uncharacterized conserved protein [Function unknown]; Region: COG1434 316055013738 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 316055013739 putative active site [active] 316055013740 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 316055013741 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 316055013742 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 316055013743 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 316055013744 Walker A/P-loop; other site 316055013745 ATP binding site [chemical binding]; other site 316055013746 Q-loop/lid; other site 316055013747 ABC transporter signature motif; other site 316055013748 Walker B; other site 316055013749 D-loop; other site 316055013750 H-loop/switch region; other site 316055013751 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 316055013752 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 316055013753 Response regulator receiver domain; Region: Response_reg; pfam00072 316055013754 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 316055013755 active site 316055013756 phosphorylation site [posttranslational modification] 316055013757 intermolecular recognition site; other site 316055013758 dimerization interface [polypeptide binding]; other site 316055013759 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 316055013760 tyrosine decarboxylase; Region: PLN02880 316055013761 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 316055013762 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055013763 catalytic residue [active] 316055013764 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 316055013765 Protein of unknown function (DUF964); Region: DUF964; cl01483 316055013766 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 316055013767 diaminopimelate decarboxylase; Region: lysA; TIGR01048 316055013768 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 316055013769 active site 316055013770 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 316055013771 substrate binding site [chemical binding]; other site 316055013772 catalytic residues [active] 316055013773 dimer interface [polypeptide binding]; other site 316055013774 argininosuccinate lyase; Provisional; Region: PRK00855 316055013775 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 316055013776 active sites [active] 316055013777 tetramer interface [polypeptide binding]; other site 316055013778 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 316055013779 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 316055013780 catalytic residues [active] 316055013781 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 316055013782 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 316055013783 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 316055013784 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316055013785 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 316055013786 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 316055013787 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 316055013788 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 316055013789 Ligand binding site [chemical binding]; other site 316055013790 Electron transfer flavoprotein domain; Region: ETF; pfam01012 316055013791 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 316055013792 Hypoxia induced protein conserved region; Region: HIG_1_N; pfam04588 316055013793 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 316055013794 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013795 dimer interface [polypeptide binding]; other site 316055013796 phosphorylation site [posttranslational modification] 316055013797 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 316055013798 ATP binding site [chemical binding]; other site 316055013799 Mg2+ binding site [ion binding]; other site 316055013800 G-X-G motif; other site 316055013801 Response regulator receiver domain; Region: Response_reg; pfam00072 316055013802 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 316055013803 active site 316055013804 phosphorylation site [posttranslational modification] 316055013805 intermolecular recognition site; other site 316055013806 dimerization interface [polypeptide binding]; other site 316055013807 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 316055013808 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 316055013809 active site 316055013810 HIGH motif; other site 316055013811 nucleotide binding site [chemical binding]; other site 316055013812 active site 316055013813 KMSKS motif; other site 316055013814 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316055013815 endonuclease III; Region: ENDO3c; smart00478 316055013816 minor groove reading motif; other site 316055013817 helix-hairpin-helix signature motif; other site 316055013818 substrate binding pocket [chemical binding]; other site 316055013819 active site 316055013820 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 316055013821 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 316055013822 Beta-lactamase superfamily domain; Region: Lactamase_B_3; pfam13483 316055013823 Response regulator receiver domain; Region: Response_reg; pfam00072 316055013824 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 316055013825 active site 316055013826 phosphorylation site [posttranslational modification] 316055013827 intermolecular recognition site; other site 316055013828 dimerization interface [polypeptide binding]; other site 316055013829 PAS fold; Region: PAS_4; pfam08448 316055013830 PAS fold; Region: PAS_4; pfam08448 316055013831 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 316055013832 putative active site [active] 316055013833 heme pocket [chemical binding]; other site 316055013834 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 316055013835 ATP binding site [chemical binding]; other site 316055013836 Mg2+ binding site [ion binding]; other site 316055013837 G-X-G motif; other site 316055013838 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 316055013839 active site 316055013840 phosphorylation site [posttranslational modification] 316055013841 intermolecular recognition site; other site 316055013842 dimerization interface [polypeptide binding]; other site 316055013843 PRC-barrel domain; Region: PRC; pfam05239 316055013844 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu_like; cd11331 316055013845 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 316055013846 active site 316055013847 catalytic site [active] 316055013848 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 316055013849 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 316055013850 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 316055013851 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 316055013852 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 316055013853 DNA binding site [nucleotide binding] 316055013854 active site 316055013855 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 316055013856 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 316055013857 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 316055013858 metallophosphoesterase, RPA4764 family; Region: RPA4764; TIGR03768 316055013859 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 316055013860 putative active site [active] 316055013861 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 316055013862 putative active site [active] 316055013863 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 316055013864 active site 316055013865 NTP binding site [chemical binding]; other site 316055013866 metal binding triad [ion binding]; metal-binding site 316055013867 antibiotic binding site [chemical binding]; other site 316055013868 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 316055013869 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 316055013870 trimer interface [polypeptide binding]; other site 316055013871 active site 316055013872 Deoxycytidine deaminase [Nucleotide transport and metabolism]; Region: Dcd; COG0717 316055013873 trimer interface [polypeptide binding]; other site 316055013874 active site 316055013875 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 316055013876 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 316055013877 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 316055013878 catalytic residue [active] 316055013879 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 316055013880 active site 316055013881 oxyanion hole [active] 316055013882 catalytic triad [active] 316055013883 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 316055013884 active site 316055013885 catalytic triad [active] 316055013886 oxyanion hole [active] 316055013887 OpgC protein; Region: OpgC_C; pfam10129 316055013888 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316055013889 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 316055013890 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 316055013891 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 316055013892 dimerization interface [polypeptide binding]; other site 316055013893 domain crossover interface; other site 316055013894 redox-dependent activation switch; other site 316055013895 ornithine carbamoyltransferase; Provisional; Region: PRK00779 316055013896 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316055013897 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316055013898 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 316055013899 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 316055013900 inhibitor-cofactor binding pocket; inhibition site 316055013901 pyridoxal 5'-phosphate binding site [chemical binding]; other site 316055013902 catalytic residue [active] 316055013903 GcrA cell cycle regulator; Region: GcrA; pfam07750 316055013904 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 316055013905 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 316055013906 active site 316055013907 phosphorylation site [posttranslational modification] 316055013908 intermolecular recognition site; other site 316055013909 dimerization interface [polypeptide binding]; other site 316055013910 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055013911 DNA binding site [nucleotide binding] 316055013912 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 316055013913 PhoU domain; Region: PhoU; pfam01895 316055013914 PhoU domain; Region: PhoU; pfam01895 316055013915 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 316055013916 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 316055013917 Walker A/P-loop; other site 316055013918 ATP binding site [chemical binding]; other site 316055013919 Q-loop/lid; other site 316055013920 ABC transporter signature motif; other site 316055013921 Walker B; other site 316055013922 D-loop; other site 316055013923 H-loop/switch region; other site 316055013924 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 316055013925 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055013926 dimer interface [polypeptide binding]; other site 316055013927 conserved gate region; other site 316055013928 putative PBP binding loops; other site 316055013929 ABC-ATPase subunit interface; other site 316055013930 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 316055013931 dimer interface [polypeptide binding]; other site 316055013932 conserved gate region; other site 316055013933 putative PBP binding loops; other site 316055013934 ABC-ATPase subunit interface; other site 316055013935 PBP superfamily domain; Region: PBP_like_2; cl17296 316055013936 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 316055013937 PAS domain; Region: PAS; smart00091 316055013938 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 316055013939 dimer interface [polypeptide binding]; other site 316055013940 phosphorylation site [posttranslational modification] 316055013941 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 316055013942 ATP binding site [chemical binding]; other site 316055013943 Mg2+ binding site [ion binding]; other site 316055013944 G-X-G motif; other site 316055013945 Predicted integral membrane protein [Function unknown]; Region: COG0392 316055013946 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 316055013947 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316055013948 ligand binding site [chemical binding]; other site 316055013949 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 316055013950 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 316055013951 Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; Region: CE4_Mlr8448_like_5s; cd10968 316055013952 putative active site [active] 316055013953 heat shock protein 90; Provisional; Region: PRK05218 316055013954 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 316055013955 ATP binding site [chemical binding]; other site 316055013956 Mg2+ binding site [ion binding]; other site 316055013957 G-X-G motif; other site 316055013958 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 316055013959 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 316055013960 ATP binding site [chemical binding]; other site 316055013961 Mg2+ binding site [ion binding]; other site 316055013962 G-X-G motif; other site 316055013963 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 316055013964 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 316055013965 active site 316055013966 phosphorylation site [posttranslational modification] 316055013967 intermolecular recognition site; other site 316055013968 dimerization interface [polypeptide binding]; other site 316055013969 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 316055013970 DNA binding site [nucleotide binding] 316055013971 Predicted membrane protein [Function unknown]; Region: COG3212 316055013972 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 316055013973 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 316055013974 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 316055013975 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 316055013976 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 316055013977 5'-methylthioadenosine phosphorylase; Provisional; Region: PRK08931 316055013978 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 316055013979 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 316055013980 active site 316055013981 dimer interface [polypeptide binding]; other site 316055013982 metal binding site [ion binding]; metal-binding site 316055013983 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 316055013984 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 316055013985 acyl-CoA synthetase; Provisional; Region: PRK13391 316055013986 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 316055013987 acyl-activating enzyme (AAE) consensus motif; other site 316055013988 putative AMP binding site [chemical binding]; other site 316055013989 putative active site [active] 316055013990 putative CoA binding site [chemical binding]; other site 316055013991 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 316055013992 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 316055013993 ATP binding site [chemical binding]; other site 316055013994 putative Mg++ binding site [ion binding]; other site 316055013995 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 316055013996 nucleotide binding region [chemical binding]; other site 316055013997 ATP-binding site [chemical binding]; other site 316055013998 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 316055013999 HRDC domain; Region: HRDC; pfam00570 316055014000 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; pfam09723 316055014001 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 316055014002 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 316055014003 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 316055014004 active site 316055014005 phosphorylation site [posttranslational modification] 316055014006 intermolecular recognition site; other site 316055014007 dimerization interface [polypeptide binding]; other site 316055014008 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 316055014009 Zn2+ binding site [ion binding]; other site 316055014010 Mg2+ binding site [ion binding]; other site 316055014011 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316055014012 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 316055014013 SLBB domain; Region: SLBB; pfam10531 316055014014 methionine sulfoxide reductase A; Provisional; Region: PRK00058 316055014015 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239