-- dump date 20140619_224121 -- class Genbank::misc_feature -- table misc_feature_note -- id note 504832000001 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 504832000002 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 504832000003 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832000004 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 504832000005 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832000006 catalytic residue [active] 504832000007 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832000008 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 504832000009 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 504832000010 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 504832000011 ParA-like protein; Provisional; Region: PHA02518 504832000012 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 504832000013 P-loop; other site 504832000014 Magnesium ion binding site [ion binding]; other site 504832000015 Replication initiator protein A; Region: RPA; pfam10134 504832000016 Helix-turn-helix domain; Region: HTH_17; pfam12728 504832000017 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 504832000018 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832000019 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 504832000020 active site triad [active] 504832000021 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 504832000022 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 504832000023 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 504832000024 metal-binding site [ion binding] 504832000025 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832000026 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 504832000027 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 504832000028 DNA binding residues [nucleotide binding] 504832000029 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 504832000030 dimer interface [polypeptide binding]; other site 504832000031 putative metal binding site [ion binding]; other site 504832000032 Predicted metal-binding protein [General function prediction only]; Region: COG3019 504832000033 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 504832000034 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 504832000035 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832000036 YtkA-like; Region: YtkA; pfam13115 504832000037 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 504832000038 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832000039 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 504832000040 arsenical-resistance protein; Region: acr3; TIGR00832 504832000041 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 504832000042 ArsC family; Region: ArsC; pfam03960 504832000043 catalytic residues [active] 504832000044 Low molecular weight phosphatase family; Region: LMWPc; cl00105 504832000045 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 504832000046 active site 504832000047 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 504832000048 dimerization interface [polypeptide binding]; other site 504832000049 putative DNA binding site [nucleotide binding]; other site 504832000050 putative Zn2+ binding site [ion binding]; other site 504832000051 Domain of unknown function DUF87; Region: DUF87; pfam01935 504832000052 HerA helicase [Replication, recombination, and repair]; Region: COG0433 504832000053 SIR2-like domain; Region: SIR2_2; pfam13289 504832000054 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 504832000055 oligomeric interface; other site 504832000056 putative active site [active] 504832000057 homodimer interface [polypeptide binding]; other site 504832000058 Helix-turn-helix domain; Region: HTH_17; pfam12728 504832000059 MarR family; Region: MarR_2; pfam12802 504832000060 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Region: PLDc_unchar5; cd09133 504832000061 PLD-like domain; Region: PLDc_2; pfam13091 504832000062 putative active site [active] 504832000063 putative catalytic site [active] 504832000064 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Region: PLDc_unchar5; cd09133 504832000065 PLD-like domain; Region: PLDc_2; pfam13091 504832000066 putative active site [active] 504832000067 putative catalytic site [active] 504832000068 AAA domain; Region: AAA_11; pfam13086 504832000069 Part of AAA domain; Region: AAA_19; pfam13245 504832000070 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 504832000071 AAA domain; Region: AAA_12; pfam13087 504832000072 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 504832000073 MPN+ (JAMM) motif; other site 504832000074 Zinc-binding site [ion binding]; other site 504832000075 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 504832000076 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 504832000077 putative ligand binding site [chemical binding]; other site 504832000078 NAD binding site [chemical binding]; other site 504832000079 catalytic site [active] 504832000080 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832000081 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 504832000082 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832000083 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832000084 Walker A/P-loop; other site 504832000085 ATP binding site [chemical binding]; other site 504832000086 Q-loop/lid; other site 504832000087 ABC transporter signature motif; other site 504832000088 Walker B; other site 504832000089 D-loop; other site 504832000090 H-loop/switch region; other site 504832000091 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 504832000092 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 504832000093 Creatinine amidohydrolase; Region: Creatininase; pfam02633 504832000094 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832000095 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 504832000096 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 504832000097 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 504832000098 active site 504832000099 FMN binding site [chemical binding]; other site 504832000100 substrate binding site [chemical binding]; other site 504832000101 3Fe-4S cluster binding site [ion binding]; other site 504832000102 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 504832000103 dimer interface [polypeptide binding]; other site 504832000104 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832000105 metal binding site [ion binding]; metal-binding site 504832000106 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 504832000107 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 504832000108 Predicted membrane protein [Function unknown]; Region: COG2261 504832000109 Staphylococcal nuclease homologues; Region: SNc; smart00318 504832000110 Catalytic site; other site 504832000111 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 504832000112 Peptidase family M48; Region: Peptidase_M48; pfam01435 504832000113 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 504832000114 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 504832000115 Ferredoxin [Energy production and conversion]; Region: COG1146 504832000116 4Fe-4S binding domain; Region: Fer4; cl02805 504832000117 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 504832000118 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 504832000119 RNA binding surface [nucleotide binding]; other site 504832000120 DEAD/DEAH box helicase; Region: DEAD; pfam00270 504832000121 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 504832000122 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 504832000123 nucleotide binding region [chemical binding]; other site 504832000124 ATP-binding site [chemical binding]; other site 504832000125 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 504832000126 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 504832000127 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832000128 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832000129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 504832000130 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 504832000131 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 504832000132 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 504832000133 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 504832000134 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 504832000135 metal ion-dependent adhesion site (MIDAS); other site 504832000136 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 504832000137 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 504832000138 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 504832000139 DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: CbpA; COG2214 504832000140 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 504832000141 HSP70 interaction site [polypeptide binding]; other site 504832000142 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 504832000143 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 504832000144 Transporter associated domain; Region: CorC_HlyC; smart01091 504832000145 Domain of unknown function DUF21; Region: DUF21; pfam01595 504832000146 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 504832000147 active site 504832000148 dimer interface [polypeptide binding]; other site 504832000149 metal binding site [ion binding]; metal-binding site 504832000150 shikimate kinase; Provisional; Region: PRK13946 504832000151 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 504832000152 ADP binding site [chemical binding]; other site 504832000153 magnesium binding site [ion binding]; other site 504832000154 putative shikimate binding site; other site 504832000155 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 504832000156 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 504832000157 active site 504832000158 DNA binding site [nucleotide binding] 504832000159 Int/Topo IB signature motif; other site 504832000160 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 504832000161 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 504832000162 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 504832000163 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 504832000164 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 504832000165 ATP binding site [chemical binding]; other site 504832000166 putative Mg++ binding site [ion binding]; other site 504832000167 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 504832000168 SEC-C motif; Region: SEC-C; pfam02810 504832000169 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 504832000170 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 504832000171 heterotetramer interface [polypeptide binding]; other site 504832000172 active site pocket [active] 504832000173 cleavage site 504832000174 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 504832000175 active site 504832000176 8-oxo-dGMP binding site [chemical binding]; other site 504832000177 nudix motif; other site 504832000178 metal binding site [ion binding]; metal-binding site 504832000179 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 504832000180 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 504832000181 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832000182 active site 504832000183 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 504832000184 GSH binding site [chemical binding]; other site 504832000185 catalytic residues [active] 504832000186 nitrilase; Region: PLN02798 504832000187 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 504832000188 putative active site [active] 504832000189 catalytic triad [active] 504832000190 dimer interface [polypeptide binding]; other site 504832000191 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 504832000192 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 504832000193 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 504832000194 S-adenosylmethionine binding site [chemical binding]; other site 504832000195 Bacterial PH domain; Region: DUF304; pfam03703 504832000196 aspartate kinase; Reviewed; Region: PRK06635 504832000197 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 504832000198 putative nucleotide binding site [chemical binding]; other site 504832000199 putative catalytic residues [active] 504832000200 putative Mg ion binding site [ion binding]; other site 504832000201 putative aspartate binding site [chemical binding]; other site 504832000202 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 504832000203 putative allosteric regulatory site; other site 504832000204 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 504832000205 putative allosteric regulatory residue; other site 504832000206 MarC family integral membrane protein; Region: MarC; cl00919 504832000207 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 504832000208 GAF domain; Region: GAF; pfam01590 504832000209 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 504832000210 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 504832000211 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 504832000212 peptide chain release factor 1; Validated; Region: prfA; PRK00591 504832000213 This domain is found in peptide chain release factors; Region: PCRF; smart00937 504832000214 RF-1 domain; Region: RF-1; pfam00472 504832000215 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 504832000216 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 504832000217 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 504832000218 Methyltransferase domain; Region: Methyltransf_23; pfam13489 504832000219 Methyltransferase domain; Region: Methyltransf_11; pfam08241 504832000220 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 504832000221 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 504832000222 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 504832000223 Amidase; Region: Amidase; pfam01425 504832000224 EamA-like transporter family; Region: EamA; pfam00892 504832000225 aromatic amino acid exporter; Provisional; Region: PRK11689 504832000226 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 504832000227 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 504832000228 NAD(P) binding site [chemical binding]; other site 504832000229 homotetramer interface [polypeptide binding]; other site 504832000230 homodimer interface [polypeptide binding]; other site 504832000231 active site 504832000232 putative acyltransferase; Provisional; Region: PRK05790 504832000233 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 504832000234 dimer interface [polypeptide binding]; other site 504832000235 active site 504832000236 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 504832000237 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 504832000238 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 504832000239 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 504832000240 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832000241 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832000242 metal binding site [ion binding]; metal-binding site 504832000243 active site 504832000244 I-site; other site 504832000245 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 504832000246 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 504832000247 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 504832000248 Transglycosylase; Region: Transgly; cl17702 504832000249 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 504832000250 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 504832000251 substrate binding pocket [chemical binding]; other site 504832000252 chain length determination region; other site 504832000253 substrate-Mg2+ binding site; other site 504832000254 catalytic residues [active] 504832000255 aspartate-rich region 1; other site 504832000256 active site lid residues [active] 504832000257 aspartate-rich region 2; other site 504832000258 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 504832000259 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 504832000260 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 504832000261 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 504832000262 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 504832000263 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 504832000264 metal binding site 2 [ion binding]; metal-binding site 504832000265 putative DNA binding helix; other site 504832000266 metal binding site 1 [ion binding]; metal-binding site 504832000267 dimer interface [polypeptide binding]; other site 504832000268 structural Zn2+ binding site [ion binding]; other site 504832000269 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 504832000270 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 504832000271 active site 504832000272 nucleophile elbow; other site 504832000273 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 504832000274 MutS domain I; Region: MutS_I; pfam01624 504832000275 MutS domain II; Region: MutS_II; pfam05188 504832000276 MutS domain III; Region: MutS_III; pfam05192 504832000277 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 504832000278 Walker A/P-loop; other site 504832000279 ATP binding site [chemical binding]; other site 504832000280 Q-loop/lid; other site 504832000281 ABC transporter signature motif; other site 504832000282 Walker B; other site 504832000283 D-loop; other site 504832000284 H-loop/switch region; other site 504832000285 OsmC-like protein; Region: OsmC; pfam02566 504832000286 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832000287 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832000288 Walker A/P-loop; other site 504832000289 ATP binding site [chemical binding]; other site 504832000290 Q-loop/lid; other site 504832000291 ABC transporter signature motif; other site 504832000292 Walker B; other site 504832000293 D-loop; other site 504832000294 H-loop/switch region; other site 504832000295 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832000296 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 504832000297 dimer interface [polypeptide binding]; other site 504832000298 conserved gate region; other site 504832000299 putative PBP binding loops; other site 504832000300 ABC-ATPase subunit interface; other site 504832000301 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 504832000302 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 504832000303 substrate binding pocket [chemical binding]; other site 504832000304 membrane-bound complex binding site; other site 504832000305 hinge residues; other site 504832000306 PII uridylyl-transferase; Provisional; Region: PRK05092 504832000307 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 504832000308 metal binding triad; other site 504832000309 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 504832000310 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 504832000311 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 504832000312 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 504832000313 Transglycosylase; Region: Transgly; pfam00912 504832000314 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 504832000315 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 504832000316 Protein of unknown function DUF45; Region: DUF45; pfam01863 504832000317 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 504832000318 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 504832000319 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832000320 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 504832000321 dimer interface [polypeptide binding]; other site 504832000322 phosphorylation site [posttranslational modification] 504832000323 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 504832000324 ATP binding site [chemical binding]; other site 504832000325 Mg2+ binding site [ion binding]; other site 504832000326 G-X-G motif; other site 504832000327 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 504832000328 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832000329 active site 504832000330 phosphorylation site [posttranslational modification] 504832000331 intermolecular recognition site; other site 504832000332 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 504832000333 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; cl17299 504832000334 heme binding pocket [chemical binding]; other site 504832000335 heme ligand [chemical binding]; other site 504832000336 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 504832000337 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 504832000338 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 504832000339 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 504832000340 active site 504832000341 FMN binding site [chemical binding]; other site 504832000342 substrate binding site [chemical binding]; other site 504832000343 homotetramer interface [polypeptide binding]; other site 504832000344 catalytic residue [active] 504832000345 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 504832000346 hypothetical protein; Provisional; Region: PRK11770 504832000347 Domain of unknown function (DUF307); Region: DUF307; pfam03733 504832000348 Domain of unknown function (DUF307); Region: DUF307; pfam03733 504832000349 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 504832000350 DEAD-like helicases superfamily; Region: DEXDc; smart00487 504832000351 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 504832000352 ATP binding site [chemical binding]; other site 504832000353 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 504832000354 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 504832000355 cofactor binding site; other site 504832000356 DNA binding site [nucleotide binding] 504832000357 substrate interaction site [chemical binding]; other site 504832000358 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 504832000359 ATP binding site [chemical binding]; other site 504832000360 putative Mg++ binding site [ion binding]; other site 504832000361 helicase superfamily c-terminal domain; Region: HELICc; smart00490 504832000362 ATP-binding site [chemical binding]; other site 504832000363 Nuclease-related domain; Region: NERD; pfam08378 504832000364 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 504832000365 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832000366 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 504832000367 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 504832000368 DNA binding residues [nucleotide binding] 504832000369 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832000370 AAA domain; Region: AAA_23; pfam13476 504832000371 Walker A/P-loop; other site 504832000372 ATP binding site [chemical binding]; other site 504832000373 Protein of unknown function (DUF3732); Region: DUF3732; pfam12532 504832000374 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 504832000375 Part of AAA domain; Region: AAA_19; pfam13245 504832000376 Family description; Region: UvrD_C_2; pfam13538 504832000377 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 504832000378 AAA domain; Region: AAA_23; pfam13476 504832000379 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 504832000380 active site 504832000381 metal binding site [ion binding]; metal-binding site 504832000382 BsuBI/PstI restriction endonuclease C-terminus; Region: BsuBI_PstI_RE; pfam06616 504832000383 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family; Region: met_A_Alw26; TIGR02987 504832000384 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 504832000385 S-adenosylmethionine binding site [chemical binding]; other site 504832000386 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 504832000387 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 504832000388 non-specific DNA binding site [nucleotide binding]; other site 504832000389 salt bridge; other site 504832000390 sequence-specific DNA binding site [nucleotide binding]; other site 504832000391 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832000392 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 504832000393 putative dimer interface [polypeptide binding]; other site 504832000394 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832000395 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 504832000396 putative dimer interface [polypeptide binding]; other site 504832000397 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 504832000398 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 504832000399 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 504832000400 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 504832000401 Class I aldolases; Region: Aldolase_Class_I; cl17187 504832000402 Class I aldolases; Region: Aldolase_Class_I; cl17187 504832000403 catalytic residue [active] 504832000404 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 504832000405 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 504832000406 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832000407 Soluble P-type ATPase [General function prediction only]; Region: COG4087 504832000408 K+-transporting ATPase, c chain; Region: KdpC; cl00944 504832000409 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 504832000410 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 504832000411 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 504832000412 Ligand Binding Site [chemical binding]; other site 504832000413 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 504832000414 GAF domain; Region: GAF_3; pfam13492 504832000415 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 504832000416 dimer interface [polypeptide binding]; other site 504832000417 phosphorylation site [posttranslational modification] 504832000418 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 504832000419 ATP binding site [chemical binding]; other site 504832000420 Mg2+ binding site [ion binding]; other site 504832000421 G-X-G motif; other site 504832000422 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832000423 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832000424 active site 504832000425 phosphorylation site [posttranslational modification] 504832000426 intermolecular recognition site; other site 504832000427 dimerization interface [polypeptide binding]; other site 504832000428 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 504832000429 DNA binding site [nucleotide binding] 504832000430 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 504832000431 active site 504832000432 phosphorylation site [posttranslational modification] 504832000433 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832000434 alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins; Region: alpha-crystallin-Hsps_p23-like; cl00175 504832000435 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832000436 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832000437 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 504832000438 dimerization interface [polypeptide binding]; other site 504832000439 substrate binding pocket [chemical binding]; other site 504832000440 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 504832000441 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 504832000442 VirB7 interaction site; other site 504832000443 conjugal transfer protein TrbF; Provisional; Region: PRK13872 504832000444 conjugal transfer protein TrbL; Provisional; Region: PRK13875 504832000445 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 504832000446 conjugative transfer region protein TrbK; Region: other_trbK; TIGR04360 504832000447 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 504832000448 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 504832000449 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 504832000450 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 504832000451 Walker A motif; other site 504832000452 ATP binding site [chemical binding]; other site 504832000453 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 504832000454 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 504832000455 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 504832000456 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 504832000457 Walker A motif; other site 504832000458 ATP binding site [chemical binding]; other site 504832000459 Walker B motif; other site 504832000460 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 504832000461 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 504832000462 Walker A motif; other site 504832000463 ATP binding site [chemical binding]; other site 504832000464 Walker B motif; other site 504832000465 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 504832000466 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 504832000467 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832000468 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 504832000469 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832000470 catalytic residue [active] 504832000471 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832000472 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 504832000473 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 504832000474 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 504832000475 ParA-like protein; Provisional; Region: PHA02518 504832000476 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 504832000477 P-loop; other site 504832000478 Magnesium ion binding site [ion binding]; other site 504832000479 Replication initiator protein A; Region: RPA; pfam10134 504832000480 Helix-turn-helix domain; Region: HTH_17; pfam12728 504832000481 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 504832000482 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 504832000483 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 504832000484 non-specific DNA binding site [nucleotide binding]; other site 504832000485 salt bridge; other site 504832000486 sequence-specific DNA binding site [nucleotide binding]; other site 504832000487 Uncharacterized conserved protein [Function unknown]; Region: COG5489 504832000488 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 504832000489 Toprim domain; Region: Toprim_3; pfam13362 504832000490 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 504832000491 S-adenosylmethionine binding site [chemical binding]; other site 504832000492 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 504832000493 Helicase_C-like; Region: Helicase_C_4; pfam13871 504832000494 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 504832000495 ParB-like nuclease domain; Region: ParBc; pfam02195 504832000496 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 504832000497 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 504832000498 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 504832000499 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 504832000500 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 504832000501 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 504832000502 Superfamily II helicase [General function prediction only]; Region: COG1204 504832000503 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 504832000504 ATP binding site [chemical binding]; other site 504832000505 putative Mg++ binding site [ion binding]; other site 504832000506 Competence protein CoiA-like family; Region: CoiA; cl11541 504832000507 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 504832000508 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 504832000509 Chromate transporter; Region: Chromate_transp; pfam02417 504832000510 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 504832000511 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832000512 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 504832000513 arsenical-resistance protein; Region: acr3; TIGR00832 504832000514 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 504832000515 ArsC family; Region: ArsC; pfam03960 504832000516 catalytic residues [active] 504832000517 Low molecular weight phosphatase family; Region: LMWPc; cl00105 504832000518 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 504832000519 active site 504832000520 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 504832000521 putative DNA binding site [nucleotide binding]; other site 504832000522 putative Zn2+ binding site [ion binding]; other site 504832000523 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 504832000524 active site 504832000525 DNA binding site [nucleotide binding] 504832000526 Int/Topo IB signature motif; other site 504832000527 Protein of unknown function (DUF2464); Region: DUF2464; pfam10240 504832000528 Putative phosphatase (DUF442); Region: DUF442; cl17385 504832000529 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 504832000530 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 504832000531 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 504832000532 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 504832000533 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 504832000534 CPxP motif; other site 504832000535 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 504832000536 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832000537 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 504832000538 dimer interface [polypeptide binding]; other site 504832000539 phosphorylation site [posttranslational modification] 504832000540 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 504832000541 ATP binding site [chemical binding]; other site 504832000542 Mg2+ binding site [ion binding]; other site 504832000543 G-X-G motif; other site 504832000544 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832000545 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832000546 active site 504832000547 phosphorylation site [posttranslational modification] 504832000548 intermolecular recognition site; other site 504832000549 dimerization interface [polypeptide binding]; other site 504832000550 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 504832000551 DNA binding site [nucleotide binding] 504832000552 Predicted membrane protein [Function unknown]; Region: COG3212 504832000553 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 504832000554 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 504832000555 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 504832000556 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832000557 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 504832000558 apolar tunnel; other site 504832000559 heme binding site [chemical binding]; other site 504832000560 dimerization interface [polypeptide binding]; other site 504832000561 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 504832000562 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 504832000563 Predicted outer membrane protein [Function unknown]; Region: COG3652 504832000564 AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The...; Region: Rieske_AIFL_N; cd03478 504832000565 [2Fe-2S] cluster binding site [ion binding]; other site 504832000566 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 504832000567 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832000568 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832000569 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 504832000570 GTP cyclohydrolase I; Provisional; Region: PLN03044 504832000571 active site 504832000572 RNA polymerase sigma factor; Provisional; Region: PRK11922 504832000573 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832000574 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 504832000575 DNA binding residues [nucleotide binding] 504832000576 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 504832000577 PAS domain; Region: PAS_9; pfam13426 504832000578 putative active site [active] 504832000579 heme pocket [chemical binding]; other site 504832000580 MarR family; Region: MarR_2; pfam12802 504832000581 intracellular septation protein A; Reviewed; Region: PRK00259 504832000582 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 504832000583 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 504832000584 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 504832000585 P loop; other site 504832000586 GTP binding site [chemical binding]; other site 504832000587 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 504832000588 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 504832000589 active site 504832000590 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 504832000591 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 504832000592 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 504832000593 FeS/SAM binding site; other site 504832000594 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 504832000595 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 504832000596 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 504832000597 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 504832000598 Uncharacterized conserved protein [Function unknown]; Region: COG2968 504832000599 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 504832000600 signal recognition particle protein; Provisional; Region: PRK10867 504832000601 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 504832000602 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 504832000603 P loop; other site 504832000604 GTP binding site [chemical binding]; other site 504832000605 Signal peptide binding domain; Region: SRP_SPB; pfam02978 504832000606 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 504832000607 RimM N-terminal domain; Region: RimM; pfam01782 504832000608 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 504832000609 PRC-barrel domain; Region: PRC; pfam05239 504832000610 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 504832000611 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 504832000612 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_8; cd07246 504832000613 putative dimer interface [polypeptide binding]; other site 504832000614 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 504832000615 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 504832000616 substrate binding site [chemical binding]; other site 504832000617 ligand binding site [chemical binding]; other site 504832000618 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 504832000619 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 504832000620 substrate binding site [chemical binding]; other site 504832000621 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 504832000622 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 504832000623 active site clefts [active] 504832000624 zinc binding site [ion binding]; other site 504832000625 dimer interface [polypeptide binding]; other site 504832000626 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 504832000627 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 504832000628 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 504832000629 tartrate dehydrogenase; Region: TTC; TIGR02089 504832000630 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 504832000631 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 504832000632 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 504832000633 putative substrate translocation pore; other site 504832000634 malonyl-CoA synthase; Validated; Region: PRK07514 504832000635 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 504832000636 acyl-activating enzyme (AAE) consensus motif; other site 504832000637 active site 504832000638 AMP binding site [chemical binding]; other site 504832000639 CoA binding site [chemical binding]; other site 504832000640 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832000641 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 504832000642 Iron-sulfur protein interface; other site 504832000643 proximal quinone binding site [chemical binding]; other site 504832000644 SdhD (CybS) interface [polypeptide binding]; other site 504832000645 proximal heme binding site [chemical binding]; other site 504832000646 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 504832000647 putative SdhC subunit interface [polypeptide binding]; other site 504832000648 putative proximal heme binding site [chemical binding]; other site 504832000649 putative Iron-sulfur protein interface [polypeptide binding]; other site 504832000650 putative proximal quinone binding site; other site 504832000651 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 504832000652 L-aspartate oxidase; Provisional; Region: PRK06175 504832000653 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 504832000654 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 504832000655 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 504832000656 MAPEG family; Region: MAPEG; cl09190 504832000657 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 504832000658 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 504832000659 ligand binding site [chemical binding]; other site 504832000660 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 504832000661 argininosuccinate synthase; Provisional; Region: PRK13820 504832000662 ANP binding site [chemical binding]; other site 504832000663 Substrate Binding Site II [chemical binding]; other site 504832000664 Substrate Binding Site I [chemical binding]; other site 504832000665 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 504832000666 active site 504832000667 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 504832000668 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 504832000669 FeS/SAM binding site; other site 504832000670 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 504832000671 Uncharacterized conserved protein [Function unknown]; Region: COG3339 504832000672 pterin-4-alpha-carbinolamine dehydratase; Validated; Region: phhB; PRK00823 504832000673 aromatic arch; other site 504832000674 DCoH dimer interaction site [polypeptide binding]; other site 504832000675 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 504832000676 DCoH tetramer interaction site [polypeptide binding]; other site 504832000677 substrate binding site [chemical binding]; other site 504832000678 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 504832000679 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 504832000680 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 504832000681 G1 box; other site 504832000682 putative GEF interaction site [polypeptide binding]; other site 504832000683 GTP/Mg2+ binding site [chemical binding]; other site 504832000684 Switch I region; other site 504832000685 G2 box; other site 504832000686 G3 box; other site 504832000687 Switch II region; other site 504832000688 G4 box; other site 504832000689 G5 box; other site 504832000690 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 504832000691 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 504832000692 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832000693 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 504832000694 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 504832000695 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 504832000696 dimer interface [polypeptide binding]; other site 504832000697 substrate binding site [chemical binding]; other site 504832000698 metal binding sites [ion binding]; metal-binding site 504832000699 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 504832000700 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 504832000701 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 504832000702 homodimer interface [polypeptide binding]; other site 504832000703 NADP binding site [chemical binding]; other site 504832000704 substrate binding site [chemical binding]; other site 504832000705 hypothetical protein; Validated; Region: PRK01310 504832000706 YGGT family; Region: YGGT; pfam02325 504832000707 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 504832000708 Serine hydrolase; Region: Ser_hydrolase; cl17834 504832000709 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 504832000710 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 504832000711 classical (c) SDRs; Region: SDR_c; cd05233 504832000712 NAD(P) binding site [chemical binding]; other site 504832000713 active site 504832000714 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 504832000715 putative metal binding site [ion binding]; other site 504832000716 Fusaric acid resistance protein family; Region: FUSC; pfam04632 504832000717 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 504832000718 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 504832000719 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 504832000720 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832000721 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832000722 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832000723 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832000724 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 504832000725 substrate binding pocket [chemical binding]; other site 504832000726 dimerization interface [polypeptide binding]; other site 504832000727 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832000728 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832000729 metal binding site [ion binding]; metal-binding site 504832000730 active site 504832000731 I-site; other site 504832000732 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 504832000733 HemY protein N-terminus; Region: HemY_N; pfam07219 504832000734 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 504832000735 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 504832000736 active site 504832000737 UGMP family protein; Validated; Region: PRK09604 504832000738 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 504832000739 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 504832000740 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 504832000741 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 504832000742 EVE domain; Region: EVE; pfam01878 504832000743 acetyl-CoA synthetase; Provisional; Region: PRK00174 504832000744 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 504832000745 active site 504832000746 CoA binding site [chemical binding]; other site 504832000747 acyl-activating enzyme (AAE) consensus motif; other site 504832000748 AMP binding site [chemical binding]; other site 504832000749 acetate binding site [chemical binding]; other site 504832000750 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832000751 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832000752 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 504832000753 Catalytic site; other site 504832000754 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 504832000755 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 504832000756 NusB family; Region: NusB; pfam01029 504832000757 16S rRNA methyltransferase B; Provisional; Region: PRK10901 504832000758 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 504832000759 S-adenosylmethionine binding site [chemical binding]; other site 504832000760 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 504832000761 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 504832000762 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 504832000763 purine monophosphate binding site [chemical binding]; other site 504832000764 dimer interface [polypeptide binding]; other site 504832000765 putative catalytic residues [active] 504832000766 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 504832000767 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 504832000768 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 504832000769 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 504832000770 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 504832000771 short chain dehydrogenase; Provisional; Region: PRK08278 504832000772 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832000773 NAD(P) binding site [chemical binding]; other site 504832000774 active site 504832000775 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; pfam09998 504832000776 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 504832000777 Protein of unknown function (DUF1810); Region: DUF1810; pfam08837 504832000778 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 504832000779 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 504832000780 catalytic residues [active] 504832000781 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 504832000782 Uncharacterized conserved protein [Function unknown]; Region: COG2835 504832000783 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07333 504832000784 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 504832000785 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 504832000786 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 504832000787 active site 504832000788 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 504832000789 catalytic triad [active] 504832000790 dimer interface [polypeptide binding]; other site 504832000791 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 504832000792 Nitrogen regulatory protein P-II; Region: P-II; smart00938 504832000793 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 504832000794 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 504832000795 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 504832000796 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832000797 homodimer interface [polypeptide binding]; other site 504832000798 catalytic residue [active] 504832000799 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 504832000800 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 504832000801 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 504832000802 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 504832000803 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 504832000804 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 504832000805 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 504832000806 putative catalytic site [active] 504832000807 putative phosphate binding site [ion binding]; other site 504832000808 active site 504832000809 metal binding site A [ion binding]; metal-binding site 504832000810 DNA binding site [nucleotide binding] 504832000811 putative AP binding site [nucleotide binding]; other site 504832000812 putative metal binding site B [ion binding]; other site 504832000813 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 504832000814 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 504832000815 ligand binding site [chemical binding]; other site 504832000816 flexible hinge region; other site 504832000817 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832000818 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832000819 active site 504832000820 phosphorylation site [posttranslational modification] 504832000821 intermolecular recognition site; other site 504832000822 dimerization interface [polypeptide binding]; other site 504832000823 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 504832000824 DNA binding site [nucleotide binding] 504832000825 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 504832000826 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 504832000827 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 504832000828 catalytic residue [active] 504832000829 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 504832000830 dimerization interface [polypeptide binding]; other site 504832000831 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832000832 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832000833 metal binding site [ion binding]; metal-binding site 504832000834 active site 504832000835 I-site; other site 504832000836 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 504832000837 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 504832000838 HIGH motif; other site 504832000839 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 504832000840 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 504832000841 active site 504832000842 KMSKS motif; other site 504832000843 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 504832000844 tRNA binding surface [nucleotide binding]; other site 504832000845 Lipopolysaccharide-assembly; Region: LptE; cl01125 504832000846 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 504832000847 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 504832000848 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 504832000849 ParB-like nuclease domain; Region: ParBc; pfam02195 504832000850 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 504832000851 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 504832000852 P-loop; other site 504832000853 Magnesium ion binding site [ion binding]; other site 504832000854 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 504832000855 Magnesium ion binding site [ion binding]; other site 504832000856 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 504832000857 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 504832000858 S-adenosylmethionine binding site [chemical binding]; other site 504832000859 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 504832000860 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 504832000861 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 504832000862 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 504832000863 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 504832000864 trmE is a tRNA modification GTPase; Region: trmE; cd04164 504832000865 G1 box; other site 504832000866 GTP/Mg2+ binding site [chemical binding]; other site 504832000867 Switch I region; other site 504832000868 G2 box; other site 504832000869 Switch II region; other site 504832000870 G3 box; other site 504832000871 G4 box; other site 504832000872 G5 box; other site 504832000873 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 504832000874 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 504832000875 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 504832000876 catalytic residues [active] 504832000877 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 504832000878 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832000879 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 504832000880 ABC-ATPase subunit interface; other site 504832000881 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832000882 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832000883 Walker A/P-loop; other site 504832000884 ATP binding site [chemical binding]; other site 504832000885 Q-loop/lid; other site 504832000886 ABC transporter signature motif; other site 504832000887 Walker B; other site 504832000888 D-loop; other site 504832000889 H-loop/switch region; other site 504832000890 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 504832000891 NMT1-like family; Region: NMT1_2; pfam13379 504832000892 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 504832000893 tartrate dehydrogenase; Region: TTC; TIGR02089 504832000894 Cupin domain; Region: Cupin_2; pfam07883 504832000895 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 504832000896 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 504832000897 putative ligand binding site [chemical binding]; other site 504832000898 NAD binding site [chemical binding]; other site 504832000899 catalytic site [active] 504832000900 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832000901 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 504832000902 putative C-terminal domain interface [polypeptide binding]; other site 504832000903 putative GSH binding site (G-site) [chemical binding]; other site 504832000904 putative dimer interface [polypeptide binding]; other site 504832000905 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 504832000906 dimer interface [polypeptide binding]; other site 504832000907 N-terminal domain interface [polypeptide binding]; other site 504832000908 putative substrate binding pocket (H-site) [chemical binding]; other site 504832000909 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 504832000910 non-specific DNA binding site [nucleotide binding]; other site 504832000911 salt bridge; other site 504832000912 sequence-specific DNA binding site [nucleotide binding]; other site 504832000913 Cupin domain; Region: Cupin_2; pfam07883 504832000914 transcription termination factor Rho; Provisional; Region: rho; PRK09376 504832000915 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 504832000916 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 504832000917 RNA binding site [nucleotide binding]; other site 504832000918 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 504832000919 multimer interface [polypeptide binding]; other site 504832000920 Walker A motif; other site 504832000921 ATP binding site [chemical binding]; other site 504832000922 Walker B motif; other site 504832000923 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 504832000924 PEP synthetase regulatory protein; Provisional; Region: PRK05339 504832000925 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 504832000926 active site 504832000927 dimer interface [polypeptide binding]; other site 504832000928 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 504832000929 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 504832000930 CoA-binding site [chemical binding]; other site 504832000931 ATP-binding [chemical binding]; other site 504832000932 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 504832000933 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 504832000934 active site 504832000935 catalytic site [active] 504832000936 substrate binding site [chemical binding]; other site 504832000937 preprotein translocase subunit SecB; Validated; Region: PRK05751 504832000938 SecA binding site; other site 504832000939 Preprotein binding site; other site 504832000940 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 504832000941 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 504832000942 MltA specific insert domain; Region: MltA; smart00925 504832000943 3D domain; Region: 3D; pfam06725 504832000944 Smr domain; Region: Smr; pfam01713 504832000945 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 504832000946 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 504832000947 Walker A motif; other site 504832000948 ATP binding site [chemical binding]; other site 504832000949 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 504832000950 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 504832000951 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 504832000952 active site 504832000953 HslU subunit interaction site [polypeptide binding]; other site 504832000954 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 504832000955 putative active site pocket [active] 504832000956 4-fold oligomerization interface [polypeptide binding]; other site 504832000957 metal binding residues [ion binding]; metal-binding site 504832000958 3-fold/trimer interface [polypeptide binding]; other site 504832000959 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 504832000960 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 504832000961 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 504832000962 putative active site [active] 504832000963 oxyanion strand; other site 504832000964 catalytic triad [active] 504832000965 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 504832000966 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 504832000967 catalytic residues [active] 504832000968 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 504832000969 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 504832000970 substrate binding site [chemical binding]; other site 504832000971 glutamase interaction surface [polypeptide binding]; other site 504832000972 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 504832000973 metal binding site [ion binding]; metal-binding site 504832000974 pantothenate kinase; Provisional; Region: PRK05439 504832000975 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 504832000976 ATP-binding site [chemical binding]; other site 504832000977 CoA-binding site [chemical binding]; other site 504832000978 Mg2+-binding site [ion binding]; other site 504832000979 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 504832000980 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 504832000981 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 504832000982 putative active site [active] 504832000983 heme pocket [chemical binding]; other site 504832000984 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 504832000985 dimer interface [polypeptide binding]; other site 504832000986 phosphorylation site [posttranslational modification] 504832000987 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 504832000988 ATP binding site [chemical binding]; other site 504832000989 Mg2+ binding site [ion binding]; other site 504832000990 G-X-G motif; other site 504832000991 Response regulator receiver domain; Region: Response_reg; pfam00072 504832000992 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832000993 active site 504832000994 phosphorylation site [posttranslational modification] 504832000995 intermolecular recognition site; other site 504832000996 dimerization interface [polypeptide binding]; other site 504832000997 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 504832000998 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 504832000999 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 504832001000 Walker A motif; other site 504832001001 ATP binding site [chemical binding]; other site 504832001002 Walker B motif; other site 504832001003 arginine finger; other site 504832001004 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 504832001005 Recombination, repair and ssDNA binding protein UvsY; Region: UvsY; pfam11056 504832001006 glutathione synthetase; Provisional; Region: PRK05246 504832001007 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 504832001008 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 504832001009 hypothetical protein; Reviewed; Region: PRK12497 504832001010 Predicted methyltransferases [General function prediction only]; Region: COG0313 504832001011 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 504832001012 putative SAM binding site [chemical binding]; other site 504832001013 putative homodimer interface [polypeptide binding]; other site 504832001014 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832001015 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 504832001016 putative ligand binding site [chemical binding]; other site 504832001017 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 504832001018 HemN C-terminal domain; Region: HemN_C; pfam06969 504832001019 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 504832001020 active site 504832001021 dimerization interface [polypeptide binding]; other site 504832001022 ribonuclease PH; Reviewed; Region: rph; PRK00173 504832001023 Ribonuclease PH; Region: RNase_PH_bact; cd11362 504832001024 hexamer interface [polypeptide binding]; other site 504832001025 active site 504832001026 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 504832001027 heat shock protein GrpE; Provisional; Region: PRK14141 504832001028 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 504832001029 dimer interface [polypeptide binding]; other site 504832001030 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 504832001031 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 504832001032 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 504832001033 nucleotide binding site [chemical binding]; other site 504832001034 NEF interaction site [polypeptide binding]; other site 504832001035 SBD interface [polypeptide binding]; other site 504832001036 chaperone protein DnaJ; Provisional; Region: PRK10767 504832001037 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 504832001038 HSP70 interaction site [polypeptide binding]; other site 504832001039 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 504832001040 substrate binding site [polypeptide binding]; other site 504832001041 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 504832001042 Zn binding sites [ion binding]; other site 504832001043 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 504832001044 dimer interface [polypeptide binding]; other site 504832001045 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 504832001046 S-adenosylmethionine binding site [chemical binding]; other site 504832001047 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 504832001048 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832001049 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 504832001050 active site 504832001051 dimer interface [polypeptide binding]; other site 504832001052 dihydrodipicolinate reductase; Provisional; Region: PRK00048 504832001053 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 504832001054 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 504832001055 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 504832001056 catalytic core [active] 504832001057 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 504832001058 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 504832001059 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 504832001060 DNA binding site [nucleotide binding] 504832001061 active site 504832001062 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 504832001063 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 504832001064 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 504832001065 minor groove reading motif; other site 504832001066 helix-hairpin-helix signature motif; other site 504832001067 substrate binding pocket [chemical binding]; other site 504832001068 active site 504832001069 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 504832001070 CysZ-like protein; Reviewed; Region: PRK12768 504832001071 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 504832001072 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 504832001073 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 504832001074 TAP-like protein; Region: Abhydrolase_4; pfam08386 504832001075 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 504832001076 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832001077 Walker A/P-loop; other site 504832001078 ATP binding site [chemical binding]; other site 504832001079 Q-loop/lid; other site 504832001080 ABC transporter signature motif; other site 504832001081 Walker B; other site 504832001082 D-loop; other site 504832001083 H-loop/switch region; other site 504832001084 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 504832001085 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832001086 Walker A/P-loop; other site 504832001087 ATP binding site [chemical binding]; other site 504832001088 Q-loop/lid; other site 504832001089 ABC transporter signature motif; other site 504832001090 Walker B; other site 504832001091 D-loop; other site 504832001092 H-loop/switch region; other site 504832001093 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832001094 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 504832001095 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 504832001096 dimer interface [polypeptide binding]; other site 504832001097 conserved gate region; other site 504832001098 putative PBP binding loops; other site 504832001099 ABC-ATPase subunit interface; other site 504832001100 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 504832001101 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 504832001102 dimer interface [polypeptide binding]; other site 504832001103 conserved gate region; other site 504832001104 putative PBP binding loops; other site 504832001105 ABC-ATPase subunit interface; other site 504832001106 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 504832001107 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_10; cd08515 504832001108 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832001109 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832001110 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 504832001111 dimerization interface [polypeptide binding]; other site 504832001112 Protein of unknown function (DUF1551); Region: DUF1551; pfam07585 504832001113 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 504832001114 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 504832001115 putative tRNA-binding site [nucleotide binding]; other site 504832001116 B3/4 domain; Region: B3_4; pfam03483 504832001117 tRNA synthetase B5 domain; Region: B5; smart00874 504832001118 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 504832001119 dimer interface [polypeptide binding]; other site 504832001120 motif 1; other site 504832001121 motif 3; other site 504832001122 motif 2; other site 504832001123 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 504832001124 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 504832001125 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 504832001126 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 504832001127 dimer interface [polypeptide binding]; other site 504832001128 motif 1; other site 504832001129 active site 504832001130 motif 2; other site 504832001131 motif 3; other site 504832001132 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 504832001133 23S rRNA binding site [nucleotide binding]; other site 504832001134 L21 binding site [polypeptide binding]; other site 504832001135 L13 binding site [polypeptide binding]; other site 504832001136 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 504832001137 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 504832001138 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 504832001139 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 504832001140 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832001141 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 504832001142 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 504832001143 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832001144 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 504832001145 C-terminal domain interface [polypeptide binding]; other site 504832001146 GSH binding site (G-site) [chemical binding]; other site 504832001147 dimer interface [polypeptide binding]; other site 504832001148 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 504832001149 N-terminal domain interface [polypeptide binding]; other site 504832001150 dimer interface [polypeptide binding]; other site 504832001151 substrate binding pocket (H-site) [chemical binding]; other site 504832001152 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 504832001153 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 504832001154 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 504832001155 putative NAD(P) binding site [chemical binding]; other site 504832001156 active site 504832001157 PAS domain; Region: PAS_9; pfam13426 504832001158 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 504832001159 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832001160 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832001161 metal binding site [ion binding]; metal-binding site 504832001162 active site 504832001163 I-site; other site 504832001164 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 504832001165 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 504832001166 Chromate transporter; Region: Chromate_transp; pfam02417 504832001167 Domain of Unknown Function (DUF930); Region: DUF930; pfam06059 504832001168 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 504832001169 homodimer interface [polypeptide binding]; other site 504832001170 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 504832001171 active site pocket [active] 504832001172 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 504832001173 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 504832001174 catalytic site [active] 504832001175 putative active site [active] 504832001176 putative substrate binding site [chemical binding]; other site 504832001177 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 504832001178 OstA-like protein; Region: OstA; pfam03968 504832001179 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 504832001180 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 504832001181 Walker A/P-loop; other site 504832001182 ATP binding site [chemical binding]; other site 504832001183 Q-loop/lid; other site 504832001184 ABC transporter signature motif; other site 504832001185 Walker B; other site 504832001186 D-loop; other site 504832001187 H-loop/switch region; other site 504832001188 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 504832001189 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 504832001190 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 504832001191 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 504832001192 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 504832001193 30S subunit binding site; other site 504832001194 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 504832001195 active site 504832001196 phosphorylation site [posttranslational modification] 504832001197 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 504832001198 Protein of unknown function (DUF1150); Region: DUF1150; pfam06620 504832001199 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832001200 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 504832001201 putative dimer interface [polypeptide binding]; other site 504832001202 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 504832001203 TIGR02300 family protein; Region: FYDLN_acid 504832001204 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 504832001205 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 504832001206 hinge; other site 504832001207 active site 504832001208 Zeta toxin; Region: Zeta_toxin; pfam06414 504832001209 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 504832001210 cytidylate kinase; Provisional; Region: cmk; PRK00023 504832001211 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 504832001212 CMP-binding site; other site 504832001213 The sites determining sugar specificity; other site 504832001214 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 504832001215 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 504832001216 RNA binding site [nucleotide binding]; other site 504832001217 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 504832001218 RNA binding site [nucleotide binding]; other site 504832001219 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 504832001220 RNA binding site [nucleotide binding]; other site 504832001221 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 504832001222 RNA binding site [nucleotide binding]; other site 504832001223 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 504832001224 RNA binding site [nucleotide binding]; other site 504832001225 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 504832001226 RNA binding site [nucleotide binding]; other site 504832001227 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 504832001228 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 504832001229 tandem repeat interface [polypeptide binding]; other site 504832001230 oligomer interface [polypeptide binding]; other site 504832001231 active site residues [active] 504832001232 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 504832001233 IHF dimer interface [polypeptide binding]; other site 504832001234 IHF - DNA interface [nucleotide binding]; other site 504832001235 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 504832001236 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 504832001237 active site 504832001238 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 504832001239 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 504832001240 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832001241 catalytic residue [active] 504832001242 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 504832001243 substrate binding site [chemical binding]; other site 504832001244 active site 504832001245 catalytic residues [active] 504832001246 heterodimer interface [polypeptide binding]; other site 504832001247 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 504832001248 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 504832001249 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 504832001250 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 504832001251 catalytic residues [active] 504832001252 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 504832001253 Family description; Region: UvrD_C_2; pfam13538 504832001254 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 504832001255 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 504832001256 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 504832001257 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 504832001258 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 504832001259 Substrate binding site; other site 504832001260 metal-binding site 504832001261 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 504832001262 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 504832001263 Phosphotransferase enzyme family; Region: APH; pfam01636 504832001264 PAS fold; Region: PAS_7; pfam12860 504832001265 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 504832001266 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 504832001267 dimer interface [polypeptide binding]; other site 504832001268 phosphorylation site [posttranslational modification] 504832001269 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 504832001270 ATP binding site [chemical binding]; other site 504832001271 Mg2+ binding site [ion binding]; other site 504832001272 G-X-G motif; other site 504832001273 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 504832001274 trimer interface [polypeptide binding]; other site 504832001275 active site 504832001276 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional; Region: PRK13982 504832001277 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 504832001278 Flavoprotein; Region: Flavoprotein; pfam02441 504832001279 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 504832001280 ABC1 family; Region: ABC1; cl17513 504832001281 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 504832001282 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 504832001283 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 504832001284 S-adenosylmethionine binding site [chemical binding]; other site 504832001285 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 504832001286 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 504832001287 DNA binding site [nucleotide binding] 504832001288 catalytic residue [active] 504832001289 H2TH interface [polypeptide binding]; other site 504832001290 putative catalytic residues [active] 504832001291 turnover-facilitating residue; other site 504832001292 intercalation triad [nucleotide binding]; other site 504832001293 8OG recognition residue [nucleotide binding]; other site 504832001294 putative reading head residues; other site 504832001295 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 504832001296 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 504832001297 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 504832001298 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 504832001299 ATP binding site [chemical binding]; other site 504832001300 substrate interface [chemical binding]; other site 504832001301 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 504832001302 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 504832001303 dimerization interface [polypeptide binding]; other site 504832001304 ligand binding site [chemical binding]; other site 504832001305 NADP binding site [chemical binding]; other site 504832001306 catalytic site [active] 504832001307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 504832001308 Bacterial SH3 domain; Region: SH3_4; pfam06347 504832001309 Bacterial SH3 domain; Region: SH3_4; pfam06347 504832001310 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 504832001311 metal binding site 2 [ion binding]; metal-binding site 504832001312 putative DNA binding helix; other site 504832001313 metal binding site 1 [ion binding]; metal-binding site 504832001314 dimer interface [polypeptide binding]; other site 504832001315 structural Zn2+ binding site [ion binding]; other site 504832001316 3-hydroxydecanoyl-(acyl carrier protein) dehydratase; Validated; Region: PRK05174 504832001317 active site 2 [active] 504832001318 active site 1 [active] 504832001319 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 504832001320 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 504832001321 dimer interface [polypeptide binding]; other site 504832001322 active site 504832001323 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06505 504832001324 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 504832001325 NAD binding site [chemical binding]; other site 504832001326 homotetramer interface [polypeptide binding]; other site 504832001327 homodimer interface [polypeptide binding]; other site 504832001328 substrate binding site [chemical binding]; other site 504832001329 active site 504832001330 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 504832001331 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 504832001332 tetramer interface [polypeptide binding]; other site 504832001333 heme binding pocket [chemical binding]; other site 504832001334 NADPH binding site [chemical binding]; other site 504832001335 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 504832001336 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832001337 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 504832001338 dimerization interface [polypeptide binding]; other site 504832001339 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 504832001340 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 504832001341 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 504832001342 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 504832001343 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 504832001344 RNase E interface [polypeptide binding]; other site 504832001345 trimer interface [polypeptide binding]; other site 504832001346 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 504832001347 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 504832001348 RNase E interface [polypeptide binding]; other site 504832001349 trimer interface [polypeptide binding]; other site 504832001350 active site 504832001351 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 504832001352 putative nucleic acid binding region [nucleotide binding]; other site 504832001353 G-X-X-G motif; other site 504832001354 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 504832001355 RNA binding site [nucleotide binding]; other site 504832001356 domain interface; other site 504832001357 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 504832001358 16S/18S rRNA binding site [nucleotide binding]; other site 504832001359 S13e-L30e interaction site [polypeptide binding]; other site 504832001360 25S rRNA binding site [nucleotide binding]; other site 504832001361 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 504832001362 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 504832001363 RNA binding site [nucleotide binding]; other site 504832001364 active site 504832001365 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 504832001366 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 504832001367 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 504832001368 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 504832001369 G1 box; other site 504832001370 putative GEF interaction site [polypeptide binding]; other site 504832001371 GTP/Mg2+ binding site [chemical binding]; other site 504832001372 Switch I region; other site 504832001373 G2 box; other site 504832001374 G3 box; other site 504832001375 Switch II region; other site 504832001376 G4 box; other site 504832001377 G5 box; other site 504832001378 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 504832001379 Translation-initiation factor 2; Region: IF-2; pfam11987 504832001380 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 504832001381 hypothetical protein; Provisional; Region: PRK09190 504832001382 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 504832001383 putative RNA binding cleft [nucleotide binding]; other site 504832001384 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 504832001385 NusA N-terminal domain; Region: NusA_N; pfam08529 504832001386 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 504832001387 RNA binding site [nucleotide binding]; other site 504832001388 homodimer interface [polypeptide binding]; other site 504832001389 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 504832001390 G-X-X-G motif; other site 504832001391 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 504832001392 G-X-X-G motif; other site 504832001393 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 504832001394 ribosome maturation protein RimP; Reviewed; Region: PRK00092 504832001395 Sm and related proteins; Region: Sm_like; cl00259 504832001396 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 504832001397 putative oligomer interface [polypeptide binding]; other site 504832001398 putative RNA binding site [nucleotide binding]; other site 504832001399 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5330 504832001400 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 504832001401 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 504832001402 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832001403 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 504832001404 non-specific DNA binding site [nucleotide binding]; other site 504832001405 salt bridge; other site 504832001406 sequence-specific DNA binding site [nucleotide binding]; other site 504832001407 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 504832001408 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 504832001409 putative active site [active] 504832001410 catalytic triad [active] 504832001411 putative dimer interface [polypeptide binding]; other site 504832001412 FOG: CBS domain [General function prediction only]; Region: COG0517 504832001413 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 504832001414 Transporter associated domain; Region: CorC_HlyC; smart01091 504832001415 metal-binding heat shock protein; Provisional; Region: PRK00016 504832001416 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 504832001417 KH domain; Region: KH_1; pfam00013 504832001418 PhoH-like protein; Region: PhoH; pfam02562 504832001419 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 504832001420 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 504832001421 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 504832001422 FeS/SAM binding site; other site 504832001423 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 504832001424 metal binding site 2 [ion binding]; metal-binding site 504832001425 putative DNA binding helix; other site 504832001426 metal binding site 1 [ion binding]; metal-binding site 504832001427 dimer interface [polypeptide binding]; other site 504832001428 structural Zn2+ binding site [ion binding]; other site 504832001429 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 504832001430 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832001431 Coenzyme A binding pocket [chemical binding]; other site 504832001432 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 504832001433 Glycoprotease family; Region: Peptidase_M22; pfam00814 504832001434 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 504832001435 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 504832001436 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 504832001437 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 504832001438 active site 504832001439 HIGH motif; other site 504832001440 dimer interface [polypeptide binding]; other site 504832001441 KMSKS motif; other site 504832001442 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 504832001443 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 504832001444 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 504832001445 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 504832001446 substrate binding site [chemical binding]; other site 504832001447 ATP binding site [chemical binding]; other site 504832001448 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 504832001449 Pirin-related protein [General function prediction only]; Region: COG1741 504832001450 Pirin; Region: Pirin; pfam02678 504832001451 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 504832001452 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 504832001453 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 504832001454 Mg2+ binding site [ion binding]; other site 504832001455 G-X-G motif; other site 504832001456 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 504832001457 anchoring element; other site 504832001458 dimer interface [polypeptide binding]; other site 504832001459 ATP binding site [chemical binding]; other site 504832001460 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 504832001461 active site 504832001462 putative metal-binding site [ion binding]; other site 504832001463 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 504832001464 recombination protein F; Reviewed; Region: recF; PRK00064 504832001465 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832001466 Walker A/P-loop; other site 504832001467 ATP binding site [chemical binding]; other site 504832001468 Q-loop/lid; other site 504832001469 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832001470 ABC transporter signature motif; other site 504832001471 Walker B; other site 504832001472 D-loop; other site 504832001473 H-loop/switch region; other site 504832001474 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 504832001475 putative active site [active] 504832001476 DNA polymerase III subunit beta; Validated; Region: PRK05643 504832001477 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 504832001478 putative DNA binding surface [nucleotide binding]; other site 504832001479 dimer interface [polypeptide binding]; other site 504832001480 beta-clamp/clamp loader binding surface; other site 504832001481 beta-clamp/translesion DNA polymerase binding surface; other site 504832001482 DnaA N-terminal domain; Region: DnaA_N; pfam11638 504832001483 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 504832001484 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 504832001485 Walker A motif; other site 504832001486 ATP binding site [chemical binding]; other site 504832001487 Walker B motif; other site 504832001488 arginine finger; other site 504832001489 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 504832001490 DnaA box-binding interface [nucleotide binding]; other site 504832001491 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 504832001492 methionine sulfoxide reductase A; Provisional; Region: PRK00058 504832001493 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 504832001494 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 504832001495 SLBB domain; Region: SLBB; pfam10531 504832001496 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 504832001497 PAS domain; Region: PAS_9; pfam13426 504832001498 putative active site [active] 504832001499 heme pocket [chemical binding]; other site 504832001500 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 504832001501 dimer interface [polypeptide binding]; other site 504832001502 phosphorylation site [posttranslational modification] 504832001503 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 504832001504 ATP binding site [chemical binding]; other site 504832001505 G-X-G motif; other site 504832001506 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832001507 active site 504832001508 phosphorylation site [posttranslational modification] 504832001509 intermolecular recognition site; other site 504832001510 dimerization interface [polypeptide binding]; other site 504832001511 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 504832001512 Flavodoxin; Region: Flavodoxin_1; pfam00258 504832001513 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 504832001514 FAD binding pocket [chemical binding]; other site 504832001515 FAD binding motif [chemical binding]; other site 504832001516 catalytic residues [active] 504832001517 NAD binding pocket [chemical binding]; other site 504832001518 phosphate binding motif [ion binding]; other site 504832001519 beta-alpha-beta structure motif; other site 504832001520 sulfite reductase subunit beta; Provisional; Region: PRK13504 504832001521 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 504832001522 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 504832001523 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 504832001524 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 504832001525 active site residue [active] 504832001526 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 504832001527 active site residue [active] 504832001528 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 504832001529 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 504832001530 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 504832001531 substrate binding site; other site 504832001532 tetramer interface; other site 504832001533 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 504832001534 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 504832001535 NADP binding site [chemical binding]; other site 504832001536 active site 504832001537 putative substrate binding site [chemical binding]; other site 504832001538 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 504832001539 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 504832001540 NAD binding site [chemical binding]; other site 504832001541 substrate binding site [chemical binding]; other site 504832001542 homodimer interface [polypeptide binding]; other site 504832001543 active site 504832001544 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 504832001545 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 504832001546 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832001547 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 504832001548 Walker A/P-loop; other site 504832001549 ATP binding site [chemical binding]; other site 504832001550 Q-loop/lid; other site 504832001551 ABC transporter signature motif; other site 504832001552 Walker B; other site 504832001553 D-loop; other site 504832001554 H-loop/switch region; other site 504832001555 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 504832001556 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 504832001557 inhibitor-cofactor binding pocket; inhibition site 504832001558 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832001559 catalytic residue [active] 504832001560 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 504832001561 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 504832001562 active site 504832001563 Methyltransferase domain; Region: Methyltransf_24; pfam13578 504832001564 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 504832001565 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 504832001566 dimer interface [polypeptide binding]; other site 504832001567 putative PBP binding regions; other site 504832001568 ABC-ATPase subunit interface; other site 504832001569 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 504832001570 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 504832001571 Walker A/P-loop; other site 504832001572 ATP binding site [chemical binding]; other site 504832001573 Q-loop/lid; other site 504832001574 ABC transporter signature motif; other site 504832001575 Walker B; other site 504832001576 D-loop; other site 504832001577 H-loop/switch region; other site 504832001578 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 504832001579 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 504832001580 N-terminal plug; other site 504832001581 ligand-binding site [chemical binding]; other site 504832001582 Methyltransferase domain; Region: Methyltransf_31; pfam13847 504832001583 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 504832001584 S-adenosylmethionine binding site [chemical binding]; other site 504832001585 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 504832001586 Periplasmic binding protein TroA_e. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_e; cd01142 504832001587 putative ligand binding residues [chemical binding]; other site 504832001588 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 504832001589 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832001590 catalytic residues [active] 504832001591 central insert; other site 504832001592 Heme exporter protein D (CcmD); Region: CcmD; cl11475 504832001593 heme exporter protein CcmC; Region: ccmC; TIGR01191 504832001594 heme exporter protein CcmB; Region: ccmB; TIGR01190 504832001595 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 504832001596 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832001597 Walker A/P-loop; other site 504832001598 ATP binding site [chemical binding]; other site 504832001599 Q-loop/lid; other site 504832001600 ABC transporter signature motif; other site 504832001601 Walker B; other site 504832001602 D-loop; other site 504832001603 H-loop/switch region; other site 504832001604 aconitate hydratase; Validated; Region: PRK09277 504832001605 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 504832001606 substrate binding site [chemical binding]; other site 504832001607 ligand binding site [chemical binding]; other site 504832001608 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 504832001609 substrate binding site [chemical binding]; other site 504832001610 Protein of unknown function (DUF1223); Region: DUF1223; pfam06764 504832001611 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 504832001612 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 504832001613 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832001614 Coenzyme A binding pocket [chemical binding]; other site 504832001615 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 504832001616 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 504832001617 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 504832001618 FtsX-like permease family; Region: FtsX; pfam02687 504832001619 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 504832001620 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 504832001621 Walker A/P-loop; other site 504832001622 ATP binding site [chemical binding]; other site 504832001623 Q-loop/lid; other site 504832001624 ABC transporter signature motif; other site 504832001625 Walker B; other site 504832001626 D-loop; other site 504832001627 H-loop/switch region; other site 504832001628 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 504832001629 active site 504832001630 catalytic triad [active] 504832001631 oxyanion hole [active] 504832001632 switch loop; other site 504832001633 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 504832001634 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 504832001635 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 504832001636 Predicted ATPase [General function prediction only]; Region: COG1485 504832001637 malate dehydrogenase; Reviewed; Region: PRK06223 504832001638 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 504832001639 substrate binding site [chemical binding]; other site 504832001640 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832001641 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 504832001642 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 504832001643 TPP-binding site [chemical binding]; other site 504832001644 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 504832001645 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 504832001646 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 504832001647 E3 interaction surface; other site 504832001648 lipoyl attachment site [posttranslational modification]; other site 504832001649 e3 binding domain; Region: E3_binding; pfam02817 504832001650 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 504832001651 short chain dehydrogenase; Provisional; Region: PRK06123 504832001652 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832001653 NAD(P) binding site [chemical binding]; other site 504832001654 active site 504832001655 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 504832001656 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832001657 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832001658 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 504832001659 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 504832001660 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 504832001661 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 504832001662 active site 504832001663 DNA binding site [nucleotide binding] 504832001664 Int/Topo IB signature motif; other site 504832001665 primosome assembly protein PriA; Validated; Region: PRK05580 504832001666 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 504832001667 ATP binding site [chemical binding]; other site 504832001668 putative Mg++ binding site [ion binding]; other site 504832001669 helicase superfamily c-terminal domain; Region: HELICc; smart00490 504832001670 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 504832001671 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 504832001672 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 504832001673 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 504832001674 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 504832001675 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 504832001676 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 504832001677 beta subunit interaction interface [polypeptide binding]; other site 504832001678 Walker A motif; other site 504832001679 ATP binding site [chemical binding]; other site 504832001680 Walker B motif; other site 504832001681 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 504832001682 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 504832001683 core domain interface [polypeptide binding]; other site 504832001684 delta subunit interface [polypeptide binding]; other site 504832001685 epsilon subunit interface [polypeptide binding]; other site 504832001686 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 504832001687 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 504832001688 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 504832001689 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 504832001690 alpha subunit interaction interface [polypeptide binding]; other site 504832001691 Walker A motif; other site 504832001692 ATP binding site [chemical binding]; other site 504832001693 Walker B motif; other site 504832001694 inhibitor binding site; inhibition site 504832001695 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 504832001696 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13448 504832001697 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 504832001698 gamma subunit interface [polypeptide binding]; other site 504832001699 epsilon subunit interface [polypeptide binding]; other site 504832001700 LBP interface [polypeptide binding]; other site 504832001701 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 504832001702 putative active site [active] 504832001703 Ap4A binding site [chemical binding]; other site 504832001704 nudix motif; other site 504832001705 putative metal binding site [ion binding]; other site 504832001706 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 504832001707 NodB motif; other site 504832001708 putative active site [active] 504832001709 putative catalytic site [active] 504832001710 Zn binding site [ion binding]; other site 504832001711 maltose O-acetyltransferase; Provisional; Region: PRK10092 504832001712 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 504832001713 active site 504832001714 substrate binding site [chemical binding]; other site 504832001715 trimer interface [polypeptide binding]; other site 504832001716 CoA binding site [chemical binding]; other site 504832001717 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 504832001718 C-terminal peptidase (prc); Region: prc; TIGR00225 504832001719 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 504832001720 protein binding site [polypeptide binding]; other site 504832001721 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 504832001722 Catalytic dyad [active] 504832001723 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 504832001724 Peptidase family M23; Region: Peptidase_M23; pfam01551 504832001725 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 504832001726 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 504832001727 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 504832001728 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 504832001729 active site 504832001730 (T/H)XGH motif; other site 504832001731 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 504832001732 putative catalytic cysteine [active] 504832001733 gamma-glutamyl kinase; Provisional; Region: PRK05429 504832001734 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 504832001735 nucleotide binding site [chemical binding]; other site 504832001736 homotetrameric interface [polypeptide binding]; other site 504832001737 putative phosphate binding site [ion binding]; other site 504832001738 putative allosteric binding site; other site 504832001739 PUA domain; Region: PUA; pfam01472 504832001740 GTPase CgtA; Reviewed; Region: obgE; PRK12299 504832001741 GTP1/OBG; Region: GTP1_OBG; pfam01018 504832001742 Obg GTPase; Region: Obg; cd01898 504832001743 G1 box; other site 504832001744 GTP/Mg2+ binding site [chemical binding]; other site 504832001745 Switch I region; other site 504832001746 G2 box; other site 504832001747 G3 box; other site 504832001748 Switch II region; other site 504832001749 G4 box; other site 504832001750 G5 box; other site 504832001751 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 504832001752 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 504832001753 Coenzyme A binding pocket [chemical binding]; other site 504832001754 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 504832001755 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 504832001756 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 504832001757 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 504832001758 benzoate transport; Region: 2A0115; TIGR00895 504832001759 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 504832001760 putative substrate translocation pore; other site 504832001761 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 504832001762 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 504832001763 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 504832001764 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 504832001765 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 504832001766 active site 504832001767 homotetramer interface [polypeptide binding]; other site 504832001768 Rhamnan synthesis protein F; Region: RgpF; pfam05045 504832001769 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 504832001770 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 504832001771 substrate binding site; other site 504832001772 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 504832001773 extended (e) SDRs; Region: SDR_e; cd08946 504832001774 NAD(P) binding site [chemical binding]; other site 504832001775 active site 504832001776 substrate binding site [chemical binding]; other site 504832001777 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 504832001778 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 504832001779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832001780 NAD(P) binding site [chemical binding]; other site 504832001781 active site 504832001782 Methyltransferase domain; Region: Methyltransf_23; pfam13489 504832001783 Methyltransferase domain; Region: Methyltransf_12; pfam08242 504832001784 PAS domain S-box; Region: sensory_box; TIGR00229 504832001785 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 504832001786 putative active site [active] 504832001787 heme pocket [chemical binding]; other site 504832001788 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 504832001789 Histidine kinase; Region: HisKA_3; pfam07730 504832001790 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 504832001791 ATP binding site [chemical binding]; other site 504832001792 Mg2+ binding site [ion binding]; other site 504832001793 G-X-G motif; other site 504832001794 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 504832001795 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832001796 active site 504832001797 phosphorylation site [posttranslational modification] 504832001798 intermolecular recognition site; other site 504832001799 dimerization interface [polypeptide binding]; other site 504832001800 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 504832001801 DNA binding residues [nucleotide binding] 504832001802 dimerization interface [polypeptide binding]; other site 504832001803 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 504832001804 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 504832001805 cytosine deaminase; Provisional; Region: PRK05985 504832001806 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 504832001807 active site 504832001808 Protein of unknown function, DUF488; Region: DUF488; pfam04343 504832001809 Predicted integral membrane protein [Function unknown]; Region: COG5615 504832001810 MEKHLA domain; Region: MEKHLA; pfam08670 504832001811 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_1; cd03326 504832001812 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 504832001813 putative active site pocket [active] 504832001814 metal binding site [ion binding]; metal-binding site 504832001815 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 504832001816 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 504832001817 ferrous iron transporter FeoB; Region: feoB; TIGR00437 504832001818 G1 box; other site 504832001819 GTP/Mg2+ binding site [chemical binding]; other site 504832001820 Switch I region; other site 504832001821 G2 box; other site 504832001822 G3 box; other site 504832001823 Switch II region; other site 504832001824 G4 box; other site 504832001825 G5 box; other site 504832001826 Nucleoside recognition; Region: Gate; pfam07670 504832001827 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 504832001828 Nucleoside recognition; Region: Gate; pfam07670 504832001829 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_12; cd07255 504832001830 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832001831 putative metal binding site [ion binding]; other site 504832001832 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 504832001833 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 504832001834 substrate binding pocket [chemical binding]; other site 504832001835 membrane-bound complex binding site; other site 504832001836 hinge residues; other site 504832001837 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832001838 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832001839 Protein of unknown function (DUF2474); Region: DUF2474; pfam10617 504832001840 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 504832001841 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 504832001842 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 504832001843 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 504832001844 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 504832001845 Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; Region: CE4_Mlr8448_like_5s; cd10968 504832001846 putative active site [active] 504832001847 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 504832001848 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 504832001849 ligand binding site [chemical binding]; other site 504832001850 Predicted integral membrane protein [Function unknown]; Region: COG0392 504832001851 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 504832001852 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 504832001853 dimer interface [polypeptide binding]; other site 504832001854 phosphorylation site [posttranslational modification] 504832001855 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 504832001856 ATP binding site [chemical binding]; other site 504832001857 Mg2+ binding site [ion binding]; other site 504832001858 G-X-G motif; other site 504832001859 PBP superfamily domain; Region: PBP_like_2; cl17296 504832001860 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 504832001861 dimer interface [polypeptide binding]; other site 504832001862 conserved gate region; other site 504832001863 putative PBP binding loops; other site 504832001864 ABC-ATPase subunit interface; other site 504832001865 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 504832001866 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 504832001867 dimer interface [polypeptide binding]; other site 504832001868 conserved gate region; other site 504832001869 putative PBP binding loops; other site 504832001870 ABC-ATPase subunit interface; other site 504832001871 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 504832001872 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 504832001873 Walker A/P-loop; other site 504832001874 ATP binding site [chemical binding]; other site 504832001875 Q-loop/lid; other site 504832001876 ABC transporter signature motif; other site 504832001877 Walker B; other site 504832001878 D-loop; other site 504832001879 H-loop/switch region; other site 504832001880 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 504832001881 PhoU domain; Region: PhoU; pfam01895 504832001882 PhoU domain; Region: PhoU; pfam01895 504832001883 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 504832001884 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832001885 active site 504832001886 phosphorylation site [posttranslational modification] 504832001887 intermolecular recognition site; other site 504832001888 dimerization interface [polypeptide binding]; other site 504832001889 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 504832001890 DNA binding site [nucleotide binding] 504832001891 GcrA cell cycle regulator; Region: GcrA; pfam07750 504832001892 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 504832001893 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 504832001894 inhibitor-cofactor binding pocket; inhibition site 504832001895 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832001896 catalytic residue [active] 504832001897 ornithine carbamoyltransferase; Provisional; Region: PRK00779 504832001898 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 504832001899 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 504832001900 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 504832001901 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 504832001902 dimerization interface [polypeptide binding]; other site 504832001903 domain crossover interface; other site 504832001904 redox-dependent activation switch; other site 504832001905 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 504832001906 OpgC protein; Region: OpgC_C; pfam10129 504832001907 Acyltransferase family; Region: Acyl_transf_3; pfam01757 504832001908 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 504832001909 active site 504832001910 oxyanion hole [active] 504832001911 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 504832001912 active site 504832001913 oxyanion hole [active] 504832001914 catalytic triad [active] 504832001915 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 504832001916 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 504832001917 homodimer interface [polypeptide binding]; other site 504832001918 substrate-cofactor binding pocket; other site 504832001919 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832001920 catalytic residue [active] 504832001921 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 504832001922 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 504832001923 trimer interface [polypeptide binding]; other site 504832001924 active site 504832001925 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 504832001926 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 504832001927 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 504832001928 Cu(I) binding site [ion binding]; other site 504832001929 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 504832001930 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 504832001931 CESA_like_2 is a member of the cellulose synthase superfamily; Region: CESA_like_2; cd06427 504832001932 DXD motif; other site 504832001933 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 504832001934 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 504832001935 substrate binding pocket [chemical binding]; other site 504832001936 membrane-bound complex binding site; other site 504832001937 hinge residues; other site 504832001938 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 504832001939 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 504832001940 active site 504832001941 nucleotide binding site [chemical binding]; other site 504832001942 HIGH motif; other site 504832001943 KMSKS motif; other site 504832001944 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 504832001945 putative deacylase active site [active] 504832001946 Predicted transcriptional regulator [Transcription]; Region: COG2932 504832001947 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 504832001948 Catalytic site [active] 504832001949 Protein of unknown function (DUF952); Region: DUF952; cl01393 504832001950 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 504832001951 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 504832001952 quinone interaction residues [chemical binding]; other site 504832001953 active site 504832001954 catalytic residues [active] 504832001955 FMN binding site [chemical binding]; other site 504832001956 substrate binding site [chemical binding]; other site 504832001957 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 504832001958 putative efflux protein, MATE family; Region: matE; TIGR00797 504832001959 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 504832001960 binding surface 504832001961 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 504832001962 TPR motif; other site 504832001963 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 504832001964 S-adenosylmethionine binding site [chemical binding]; other site 504832001965 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 504832001966 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 504832001967 Sel1-like repeats; Region: SEL1; smart00671 504832001968 Sel1-like repeats; Region: SEL1; smart00671 504832001969 Sel1-like repeats; Region: SEL1; smart00671 504832001970 Sel1-like repeats; Region: SEL1; smart00671 504832001971 MarR family; Region: MarR_2; pfam12802 504832001972 glutamate--cysteine ligase; Region: PLN02611 504832001973 PAN domain; Region: PAN_4; pfam14295 504832001974 Subfamily of PAN/APPLE-like domains; present in plasma prekallikrein/coagulation factor XI, microneme antigen proteins, and a few prokaryotic proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or...; Region: APPLE_Factor_XI_like; cd01100 504832001975 putative binding site; other site 504832001976 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 504832001977 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 504832001978 Catalytic site [active] 504832001979 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 504832001980 protease TldD; Provisional; Region: tldD; PRK10735 504832001981 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 504832001982 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 504832001983 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00168 504832001984 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 504832001985 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 504832001986 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 504832001987 Subunit I/III interface [polypeptide binding]; other site 504832001988 D-pathway; other site 504832001989 Subunit I/VIIc interface [polypeptide binding]; other site 504832001990 Subunit I/IV interface [polypeptide binding]; other site 504832001991 Subunit I/II interface [polypeptide binding]; other site 504832001992 Low-spin heme (heme a) binding site [chemical binding]; other site 504832001993 Subunit I/VIIa interface [polypeptide binding]; other site 504832001994 Subunit I/VIa interface [polypeptide binding]; other site 504832001995 Dimer interface; other site 504832001996 Putative water exit pathway; other site 504832001997 Binuclear center (heme a3/CuB) [ion binding]; other site 504832001998 K-pathway; other site 504832001999 Subunit I/Vb interface [polypeptide binding]; other site 504832002000 Putative proton exit pathway; other site 504832002001 Subunit I/VIb interface; other site 504832002002 Subunit I/VIc interface [polypeptide binding]; other site 504832002003 Electron transfer pathway; other site 504832002004 Subunit I/VIIIb interface [polypeptide binding]; other site 504832002005 Subunit I/VIIb interface [polypeptide binding]; other site 504832002006 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 504832002007 UbiA prenyltransferase family; Region: UbiA; pfam01040 504832002008 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 504832002009 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 504832002010 Subunit III/VIIa interface [polypeptide binding]; other site 504832002011 Phospholipid binding site [chemical binding]; other site 504832002012 Subunit I/III interface [polypeptide binding]; other site 504832002013 Subunit III/VIb interface [polypeptide binding]; other site 504832002014 Subunit III/VIa interface; other site 504832002015 Subunit III/Vb interface [polypeptide binding]; other site 504832002016 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 504832002017 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 504832002018 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 504832002019 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832002020 catalytic residue [active] 504832002021 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 504832002022 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 504832002023 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 504832002024 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 504832002025 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 504832002026 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 504832002027 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 504832002028 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 504832002029 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 504832002030 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 504832002031 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 504832002032 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 504832002033 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 504832002034 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002035 active site 504832002036 phosphorylation site [posttranslational modification] 504832002037 intermolecular recognition site; other site 504832002038 dimerization interface [polypeptide binding]; other site 504832002039 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 504832002040 DNA binding residues [nucleotide binding] 504832002041 dimerization interface [polypeptide binding]; other site 504832002042 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 504832002043 Na binding site [ion binding]; other site 504832002044 PAS fold; Region: PAS_7; pfam12860 504832002045 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832002046 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 504832002047 dimer interface [polypeptide binding]; other site 504832002048 phosphorylation site [posttranslational modification] 504832002049 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 504832002050 ATP binding site [chemical binding]; other site 504832002051 Mg2+ binding site [ion binding]; other site 504832002052 G-X-G motif; other site 504832002053 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 504832002054 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002055 active site 504832002056 phosphorylation site [posttranslational modification] 504832002057 intermolecular recognition site; other site 504832002058 dimerization interface [polypeptide binding]; other site 504832002059 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 504832002060 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002061 active site 504832002062 phosphorylation site [posttranslational modification] 504832002063 intermolecular recognition site; other site 504832002064 dimerization interface [polypeptide binding]; other site 504832002065 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 504832002066 DNA binding residues [nucleotide binding] 504832002067 dimerization interface [polypeptide binding]; other site 504832002068 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 504832002069 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 504832002070 substrate-cofactor binding pocket; other site 504832002071 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832002072 catalytic residue [active] 504832002073 biotin synthase; Region: bioB; TIGR00433 504832002074 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 504832002075 FeS/SAM binding site; other site 504832002076 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 504832002077 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832002078 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832002079 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 504832002080 dimerization interface [polypeptide binding]; other site 504832002081 class II aldolase/adducin domain protein; Provisional; Region: PRK07090 504832002082 intersubunit interface [polypeptide binding]; other site 504832002083 active site 504832002084 Zn2+ binding site [ion binding]; other site 504832002085 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 504832002086 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 504832002087 FAD binding pocket [chemical binding]; other site 504832002088 conserved FAD binding motif [chemical binding]; other site 504832002089 phosphate binding motif [ion binding]; other site 504832002090 beta-alpha-beta structure motif; other site 504832002091 NAD binding pocket [chemical binding]; other site 504832002092 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 504832002093 catalytic loop [active] 504832002094 iron binding site [ion binding]; other site 504832002095 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832002096 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 504832002097 non-specific DNA binding site [nucleotide binding]; other site 504832002098 salt bridge; other site 504832002099 sequence-specific DNA binding site [nucleotide binding]; other site 504832002100 Cupin domain; Region: Cupin_2; pfam07883 504832002101 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 504832002102 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 504832002103 conserved cys residue [active] 504832002104 metabolite-proton symporter; Region: 2A0106; TIGR00883 504832002105 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 504832002106 putative substrate translocation pore; other site 504832002107 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832002108 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 504832002109 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 504832002110 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 504832002111 SnoaL-like domain; Region: SnoaL_2; pfam12680 504832002112 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832002113 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832002114 cyanate transporter; Region: CynX; TIGR00896 504832002115 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 504832002116 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 504832002117 N-terminal plug; other site 504832002118 ligand-binding site [chemical binding]; other site 504832002119 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 504832002120 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 504832002121 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 504832002122 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 504832002123 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 504832002124 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 504832002125 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 504832002126 hinge; other site 504832002127 active site 504832002128 Protein of unknown function (DUF2948); Region: DUF2948; pfam11164 504832002129 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 504832002130 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 504832002131 NAD binding site [chemical binding]; other site 504832002132 dimerization interface [polypeptide binding]; other site 504832002133 product binding site; other site 504832002134 substrate binding site [chemical binding]; other site 504832002135 zinc binding site [ion binding]; other site 504832002136 catalytic residues [active] 504832002137 hypothetical protein; Provisional; Region: PRK02853 504832002138 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 504832002139 Low molecular weight phosphatase family; Region: LMWPc; cd00115 504832002140 active site 504832002141 Maf-like protein; Region: Maf; pfam02545 504832002142 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 504832002143 active site 504832002144 dimer interface [polypeptide binding]; other site 504832002145 zinc-binding protein; Provisional; Region: PRK01343 504832002146 PAS fold; Region: PAS_7; pfam12860 504832002147 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832002148 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832002149 metal binding site [ion binding]; metal-binding site 504832002150 active site 504832002151 I-site; other site 504832002152 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 504832002153 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 504832002154 Methyltransferase domain; Region: Methyltransf_31; pfam13847 504832002155 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 504832002156 S-adenosylmethionine binding site [chemical binding]; other site 504832002157 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 504832002158 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 504832002159 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 504832002160 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 504832002161 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 504832002162 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832002163 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK05963 504832002164 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 504832002165 dimer interface [polypeptide binding]; other site 504832002166 active site 504832002167 CoA binding pocket [chemical binding]; other site 504832002168 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 504832002169 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 504832002170 active site 504832002171 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 504832002172 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 504832002173 minor groove reading motif; other site 504832002174 helix-hairpin-helix signature motif; other site 504832002175 active site 504832002176 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 504832002177 active site 504832002178 HIGH motif; other site 504832002179 nucleotide binding site [chemical binding]; other site 504832002180 active site 504832002181 KMSKS motif; other site 504832002182 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 504832002183 dimer interface [polypeptide binding]; other site 504832002184 phosphorylation site [posttranslational modification] 504832002185 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 504832002186 ATP binding site [chemical binding]; other site 504832002187 Mg2+ binding site [ion binding]; other site 504832002188 G-X-G motif; other site 504832002189 Response regulator receiver domain; Region: Response_reg; pfam00072 504832002190 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002191 active site 504832002192 phosphorylation site [posttranslational modification] 504832002193 intermolecular recognition site; other site 504832002194 dimerization interface [polypeptide binding]; other site 504832002195 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 504832002196 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 504832002197 Ligand binding site [chemical binding]; other site 504832002198 Electron transfer flavoprotein domain; Region: ETF; pfam01012 504832002199 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 504832002200 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 504832002201 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 504832002202 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 504832002203 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 504832002204 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 504832002205 dimer interface [polypeptide binding]; other site 504832002206 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832002207 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 504832002208 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 504832002209 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832002210 catalytic residues [active] 504832002211 argininosuccinate lyase; Provisional; Region: PRK00855 504832002212 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 504832002213 active sites [active] 504832002214 tetramer interface [polypeptide binding]; other site 504832002215 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; pfam13627 504832002216 diaminopimelate decarboxylase; Region: lysA; TIGR01048 504832002217 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 504832002218 active site 504832002219 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 504832002220 substrate binding site [chemical binding]; other site 504832002221 catalytic residues [active] 504832002222 dimer interface [polypeptide binding]; other site 504832002223 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 504832002224 Response regulator receiver domain; Region: Response_reg; pfam00072 504832002225 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002226 active site 504832002227 phosphorylation site [posttranslational modification] 504832002228 intermolecular recognition site; other site 504832002229 dimerization interface [polypeptide binding]; other site 504832002230 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 504832002231 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 504832002232 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832002233 Walker A/P-loop; other site 504832002234 ATP binding site [chemical binding]; other site 504832002235 Q-loop/lid; other site 504832002236 ABC transporter signature motif; other site 504832002237 Walker B; other site 504832002238 D-loop; other site 504832002239 H-loop/switch region; other site 504832002240 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 504832002241 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 504832002242 Uncharacterized conserved protein [Function unknown]; Region: COG1434 504832002243 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 504832002244 putative active site [active] 504832002245 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 504832002246 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 504832002247 putative acyl-acceptor binding pocket; other site 504832002248 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 504832002249 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 504832002250 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 504832002251 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 504832002252 prephenate dehydrogenase; Validated; Region: PRK08507 504832002253 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 504832002254 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 504832002255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832002256 homodimer interface [polypeptide binding]; other site 504832002257 catalytic residue [active] 504832002258 hypothetical protein; Provisional; Region: PRK06034 504832002259 Chorismate mutase type II; Region: CM_2; pfam01817 504832002260 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 504832002261 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 504832002262 Methyltransferase domain; Region: Methyltransf_23; pfam13489 504832002263 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 504832002264 S-adenosylmethionine binding site [chemical binding]; other site 504832002265 TIGR02594 family protein; Region: TIGR02594 504832002266 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 504832002267 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 504832002268 MOSC domain; Region: MOSC; pfam03473 504832002269 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 504832002270 Clp amino terminal domain; Region: Clp_N; pfam02861 504832002271 Clp amino terminal domain; Region: Clp_N; pfam02861 504832002272 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 504832002273 Walker A motif; other site 504832002274 ATP binding site [chemical binding]; other site 504832002275 Walker B motif; other site 504832002276 arginine finger; other site 504832002277 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 504832002278 Walker A motif; other site 504832002279 ATP binding site [chemical binding]; other site 504832002280 Walker B motif; other site 504832002281 arginine finger; other site 504832002282 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 504832002283 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 504832002284 Peptidase family M23; Region: Peptidase_M23; pfam01551 504832002285 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 504832002286 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 504832002287 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 504832002288 catalytic residues [active] 504832002289 catalytic nucleophile [active] 504832002290 Presynaptic Site I dimer interface [polypeptide binding]; other site 504832002291 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 504832002292 Synaptic Flat tetramer interface [polypeptide binding]; other site 504832002293 Synaptic Site I dimer interface [polypeptide binding]; other site 504832002294 DNA binding site [nucleotide binding] 504832002295 Recombinase; Region: Recombinase; pfam07508 504832002296 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 504832002297 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 504832002298 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 504832002299 Domain of unknown function (DUF955); Region: DUF955; pfam06114 504832002300 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832002301 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 504832002302 non-specific DNA binding site [nucleotide binding]; other site 504832002303 salt bridge; other site 504832002304 sequence-specific DNA binding site [nucleotide binding]; other site 504832002305 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 504832002306 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832002307 AAA domain; Region: AAA_24; pfam13479 504832002308 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 504832002309 G1 box; other site 504832002310 GTP/Mg2+ binding site [chemical binding]; other site 504832002311 Switch II region; other site 504832002312 Toprim domain; Region: Toprim_3; pfam13362 504832002313 Predicted P-loop ATPase and inactivated derivatives [General function prediction only]; Region: COG5545 504832002314 Virulence-associated protein E; Region: VirE; pfam05272 504832002315 Domain of unknown function DUF302; Region: DUF302; pfam03625 504832002316 Predicted membrane protein [Function unknown]; Region: COG3462 504832002317 Short C-terminal domain; Region: SHOCT; pfam09851 504832002318 vitamin B12-dependent ribonucleotide reductase; Validated; Region: PRK06556 504832002319 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 504832002320 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 504832002321 sequence-specific DNA binding site [nucleotide binding]; other site 504832002322 salt bridge; other site 504832002323 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 504832002324 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 504832002325 ParB-like nuclease domain; Region: ParBc; pfam02195 504832002326 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 504832002327 DNA methylase; Region: N6_N4_Mtase; cl17433 504832002328 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 504832002329 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 504832002330 DNA binding site [nucleotide binding] 504832002331 substrate interaction site [chemical binding]; other site 504832002332 Hexameric tyrosine-coordinated heme protein (HTHP); Region: HTHP; pfam11534 504832002333 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 504832002334 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 504832002335 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 504832002336 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 504832002337 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 504832002338 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 504832002339 tandem repeat interface [polypeptide binding]; other site 504832002340 oligomer interface [polypeptide binding]; other site 504832002341 active site residues [active] 504832002342 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 504832002343 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 504832002344 Predicted transcriptional regulator [Transcription]; Region: COG2944 504832002345 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 504832002346 salt bridge; other site 504832002347 non-specific DNA binding site [nucleotide binding]; other site 504832002348 sequence-specific DNA binding site [nucleotide binding]; other site 504832002349 Protein of unknown function (DUF497); Region: DUF497; pfam04365 504832002350 Phage-related minor tail protein [Function unknown]; Region: COG5281 504832002351 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 504832002352 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 504832002353 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 504832002354 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 504832002355 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 504832002356 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 504832002357 NlpC/P60 family; Region: NLPC_P60; cl17555 504832002358 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 504832002359 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 504832002360 Putative phage tail protein; Region: Phage-tail_3; pfam13550 504832002361 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 504832002362 Regulatory phage protein cox; Region: Phage_Cox; pfam10743 504832002363 C1q domain; Region: C1q; cl17543 504832002364 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 504832002365 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 504832002366 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832002367 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832002368 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 504832002369 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832002370 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832002371 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 504832002372 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 504832002373 FtsX-like permease family; Region: FtsX; pfam02687 504832002374 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 504832002375 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 504832002376 Walker A/P-loop; other site 504832002377 ATP binding site [chemical binding]; other site 504832002378 Q-loop/lid; other site 504832002379 ABC transporter signature motif; other site 504832002380 Walker B; other site 504832002381 D-loop; other site 504832002382 H-loop/switch region; other site 504832002383 OsmC-like protein; Region: OsmC; pfam02566 504832002384 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 504832002385 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 504832002386 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 504832002387 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 504832002388 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 504832002389 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 504832002390 Walker A/P-loop; other site 504832002391 ATP binding site [chemical binding]; other site 504832002392 Q-loop/lid; other site 504832002393 ABC transporter signature motif; other site 504832002394 Walker B; other site 504832002395 D-loop; other site 504832002396 H-loop/switch region; other site 504832002397 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 504832002398 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 504832002399 Walker A/P-loop; other site 504832002400 ATP binding site [chemical binding]; other site 504832002401 Q-loop/lid; other site 504832002402 ABC transporter signature motif; other site 504832002403 Walker B; other site 504832002404 D-loop; other site 504832002405 H-loop/switch region; other site 504832002406 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 504832002407 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832002408 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832002409 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832002410 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832002411 Peptidase C1-like family; Region: Peptidase_C1_2; cl17447 504832002412 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 504832002413 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 504832002414 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 504832002415 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 504832002416 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 504832002417 NAD(P) binding site [chemical binding]; other site 504832002418 homotetramer interface [polypeptide binding]; other site 504832002419 homodimer interface [polypeptide binding]; other site 504832002420 active site 504832002421 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 504832002422 (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 504832002423 dimer interaction site [polypeptide binding]; other site 504832002424 substrate-binding tunnel; other site 504832002425 active site 504832002426 catalytic site [active] 504832002427 substrate binding site [chemical binding]; other site 504832002428 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 504832002429 acetate kinase; Provisional; Region: PRK07058 504832002430 propionate/acetate kinase; Provisional; Region: PRK12379 504832002431 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 504832002432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832002433 NAD(P) binding site [chemical binding]; other site 504832002434 active site 504832002435 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 504832002436 nucleophile elbow; other site 504832002437 Outer membrane efflux protein; Region: OEP; pfam02321 504832002438 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 504832002439 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 504832002440 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 504832002441 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 504832002442 dimer interface [polypeptide binding]; other site 504832002443 phosphorylation site [posttranslational modification] 504832002444 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 504832002445 Mg2+ binding site [ion binding]; other site 504832002446 G-X-G motif; other site 504832002447 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832002448 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002449 active site 504832002450 phosphorylation site [posttranslational modification] 504832002451 intermolecular recognition site; other site 504832002452 dimerization interface [polypeptide binding]; other site 504832002453 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 504832002454 DNA binding site [nucleotide binding] 504832002455 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 504832002456 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 504832002457 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 504832002458 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_like2; cd06201 504832002459 FAD binding pocket [chemical binding]; other site 504832002460 FAD binding motif [chemical binding]; other site 504832002461 catalytic residues [active] 504832002462 NAD binding pocket [chemical binding]; other site 504832002463 phosphate binding motif [ion binding]; other site 504832002464 beta-alpha-beta structure motif; other site 504832002465 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 504832002466 ApbE family; Region: ApbE; pfam02424 504832002467 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832002468 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832002469 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 504832002470 putative effector binding pocket; other site 504832002471 dimerization interface [polypeptide binding]; other site 504832002472 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 504832002473 metal-binding site [ion binding] 504832002474 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 504832002475 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832002476 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 504832002477 motif II; other site 504832002478 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 504832002479 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 504832002480 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 504832002481 Walker A/P-loop; other site 504832002482 ATP binding site [chemical binding]; other site 504832002483 Q-loop/lid; other site 504832002484 ABC transporter signature motif; other site 504832002485 Walker B; other site 504832002486 D-loop; other site 504832002487 H-loop/switch region; other site 504832002488 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 504832002489 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 504832002490 dimer interface [polypeptide binding]; other site 504832002491 putative PBP binding regions; other site 504832002492 ABC-ATPase subunit interface; other site 504832002493 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 504832002494 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 504832002495 putative hemin binding site; other site 504832002496 Hemin uptake protein hemP; Region: hemP; pfam10636 504832002497 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 504832002498 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 504832002499 N-terminal plug; other site 504832002500 ligand-binding site [chemical binding]; other site 504832002501 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 504832002502 putative heme utilization carrier protein HutX; Region: HutX; TIGR04108 504832002503 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 504832002504 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 504832002505 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832002506 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 504832002507 putative ligand binding site [chemical binding]; other site 504832002508 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 504832002509 TM-ABC transporter signature motif; other site 504832002510 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832002511 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 504832002512 TM-ABC transporter signature motif; other site 504832002513 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832002514 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832002515 Walker A/P-loop; other site 504832002516 ATP binding site [chemical binding]; other site 504832002517 Q-loop/lid; other site 504832002518 ABC transporter signature motif; other site 504832002519 Walker B; other site 504832002520 D-loop; other site 504832002521 H-loop/switch region; other site 504832002522 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832002523 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832002524 Walker A/P-loop; other site 504832002525 ATP binding site [chemical binding]; other site 504832002526 Q-loop/lid; other site 504832002527 ABC transporter signature motif; other site 504832002528 Walker B; other site 504832002529 D-loop; other site 504832002530 H-loop/switch region; other site 504832002531 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 504832002532 HIT family signature motif; other site 504832002533 catalytic residue [active] 504832002534 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 504832002535 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 504832002536 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 504832002537 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 504832002538 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 504832002539 camphor resistance protein CrcB; Provisional; Region: PRK14198 504832002540 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 504832002541 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 504832002542 ABC 3 transport family; Region: ABC-3; pfam00950 504832002543 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 504832002544 ABC-ATPase subunit interface; other site 504832002545 dimer interface [polypeptide binding]; other site 504832002546 putative PBP binding regions; other site 504832002547 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 504832002548 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 504832002549 intersubunit interface [polypeptide binding]; other site 504832002550 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 504832002551 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 504832002552 P-loop, Walker A motif; other site 504832002553 Base recognition motif; other site 504832002554 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 504832002555 FOG: WD40 repeat [General function prediction only]; Region: COG2319 504832002556 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 504832002557 structural tetrad; other site 504832002558 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 504832002559 MgtC family; Region: MgtC; pfam02308 504832002560 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 504832002561 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 504832002562 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 504832002563 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 504832002564 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 504832002565 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832002566 Coenzyme A binding pocket [chemical binding]; other site 504832002567 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 504832002568 dimer interface [polypeptide binding]; other site 504832002569 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 504832002570 active site 504832002571 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 504832002572 catalytic residues [active] 504832002573 substrate binding site [chemical binding]; other site 504832002574 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 504832002575 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 504832002576 active site 504832002577 Zn binding site [ion binding]; other site 504832002578 Protein of unknown function (DUF1007); Region: DUF1007; pfam06226 504832002579 High-affinity nickel-transport protein; Region: NicO; cl00964 504832002580 High-affinity nickel-transport protein; Region: NicO; cl00964 504832002581 ferrochelatase; Reviewed; Region: hemH; PRK00035 504832002582 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 504832002583 C-terminal domain interface [polypeptide binding]; other site 504832002584 active site 504832002585 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 504832002586 active site 504832002587 N-terminal domain interface [polypeptide binding]; other site 504832002588 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 504832002589 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 504832002590 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 504832002591 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 504832002592 trimer interface [polypeptide binding]; other site 504832002593 putative Zn binding site [ion binding]; other site 504832002594 KpsF/GutQ family protein; Region: kpsF; TIGR00393 504832002595 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 504832002596 putative active site [active] 504832002597 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 504832002598 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 504832002599 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832002600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832002601 metal binding site [ion binding]; metal-binding site 504832002602 active site 504832002603 I-site; other site 504832002604 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 504832002605 active site 504832002606 catalytic triad [active] 504832002607 oxyanion hole [active] 504832002608 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 504832002609 active site 504832002610 tetramer interface; other site 504832002611 Transglycosylase SLT domain; Region: SLT_2; pfam13406 504832002612 murein hydrolase B; Provisional; Region: PRK10760; cl17906 504832002613 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832002614 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 504832002615 active site 504832002616 oxyanion hole [active] 504832002617 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 504832002618 catalytic triad [active] 504832002619 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 504832002620 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 504832002621 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832002622 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 504832002623 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 504832002624 active site 504832002625 dimer interface [polypeptide binding]; other site 504832002626 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 504832002627 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 504832002628 active site 504832002629 FMN binding site [chemical binding]; other site 504832002630 substrate binding site [chemical binding]; other site 504832002631 3Fe-4S cluster binding site [ion binding]; other site 504832002632 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 504832002633 domain interface; other site 504832002634 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 504832002635 Uncharacterized conserved protein [Function unknown]; Region: COG2128 504832002636 RNA polymerase sigma factor SigJ; Provisional; Region: PRK09636 504832002637 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832002638 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832002639 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 504832002640 putative dimer interface [polypeptide binding]; other site 504832002641 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 504832002642 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 504832002643 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832002644 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832002645 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832002646 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 504832002647 putative dimerization interface [polypeptide binding]; other site 504832002648 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 504832002649 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 504832002650 active site 504832002651 N-formylglutamate amidohydrolase; Region: FGase; cl01522 504832002652 Response regulator receiver domain; Region: Response_reg; pfam00072 504832002653 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002654 active site 504832002655 phosphorylation site [posttranslational modification] 504832002656 intermolecular recognition site; other site 504832002657 dimerization interface [polypeptide binding]; other site 504832002658 Protein of unknown function, DUF606; Region: DUF606; pfam04657 504832002659 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 504832002660 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 504832002661 catalytic residues [active] 504832002662 catalytic nucleophile [active] 504832002663 Presynaptic Site I dimer interface [polypeptide binding]; other site 504832002664 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 504832002665 Synaptic Flat tetramer interface [polypeptide binding]; other site 504832002666 Synaptic Site I dimer interface [polypeptide binding]; other site 504832002667 DNA binding site [nucleotide binding] 504832002668 Recombinase; Region: Recombinase; pfam07508 504832002669 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 504832002670 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 504832002671 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 504832002672 AAA domain; Region: AAA_22; pfam13401 504832002673 YIEGIA protein; Region: YIEGIA; pfam14045 504832002674 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 504832002675 homotrimer interaction site [polypeptide binding]; other site 504832002676 putative active site [active] 504832002677 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 504832002678 Cupin domain; Region: Cupin_2; pfam07883 504832002679 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 504832002680 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 504832002681 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 504832002682 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 504832002683 DctM-like transporters; Region: DctM; pfam06808 504832002684 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 504832002685 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cl17315 504832002686 DNA binding residues [nucleotide binding] 504832002687 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 504832002688 Integrase core domain; Region: rve; pfam00665 504832002689 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 504832002690 Integrase core domain; Region: rve_3; pfam13683 504832002691 Transposase; Region: HTH_Tnp_1; cl17663 504832002692 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 504832002693 Helix-turn-helix domain; Region: HTH_28; pfam13518 504832002694 putative transposase OrfB; Reviewed; Region: PHA02517 504832002695 Homeodomain-like domain; Region: HTH_32; pfam13565 504832002696 Integrase core domain; Region: rve; pfam00665 504832002697 Integrase core domain; Region: rve_3; pfam13683 504832002698 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 504832002699 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 504832002700 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 504832002701 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 504832002702 dimerization interface [polypeptide binding]; other site 504832002703 metal binding site [ion binding]; metal-binding site 504832002704 DUF35 OB-fold domain; Region: DUF35; pfam01796 504832002705 acetyl-CoA acetyltransferase; Provisional; Region: PRK08142 504832002706 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 504832002707 active site 504832002708 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 504832002709 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 504832002710 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 504832002711 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 504832002712 NAD(P) binding site [chemical binding]; other site 504832002713 catalytic residues [active] 504832002714 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 504832002715 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832002716 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832002717 enoyl-CoA hydratase; Provisional; Region: PRK06494 504832002718 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 504832002719 substrate binding site [chemical binding]; other site 504832002720 oxyanion hole (OAH) forming residues; other site 504832002721 trimer interface [polypeptide binding]; other site 504832002722 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 504832002723 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832002724 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832002725 5,10-methylenetetrahydromethanopterin reductase; Region: F420_mer; TIGR03555 504832002726 N5,N10-methylenetetrahydromethanopterin reductase (Mer) catalyzes the reduction of N5,N10-methylenetetrahydromethanopterin with reduced coenzyme F420 to N5-methyltetrahydromethanopterin and oxidized coenzyme F420; Region: Tetrahydromethanopterin_reductase; cd01097 504832002727 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832002728 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832002729 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 504832002730 Predicted dinucleotide-binding enzymes [General function prediction only]; Region: COG2085 504832002731 tricarballylate dehydrogenase; Validated; Region: PRK08274 504832002732 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832002733 tricarballylate utilization protein B; Provisional; Region: PRK15033 504832002734 GTP and metal dependent enzyme involved F420 coenzyme biosynthesis (catalyzes addition of two l-glutamates to F420 precursor) [Coenzyme transport and metabolism]; Region: COG1478 504832002735 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 504832002736 LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; Region: CofD_like; cd07186 504832002737 Uncharacterized protein family UPF0052; Region: UPF0052; pfam01933 504832002738 phosphate binding site [ion binding]; other site 504832002739 dimer interface [polypeptide binding]; other site 504832002740 substrate binding site [chemical binding]; other site 504832002741 2-phospho-L-lactate guanylyltransferase; Region: F420_cofC; TIGR03552 504832002742 FO synthase; Reviewed; Region: fbiC; PRK09234 504832002743 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 504832002744 FeS/SAM binding site; other site 504832002745 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 504832002746 FeS/SAM binding site; other site 504832002747 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 504832002748 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 504832002749 putative substrate translocation pore; other site 504832002750 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 504832002751 Immunoglobulin-like domain of bacterial spore germination; Region: Gmad2; pfam10648 504832002752 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 504832002753 membrane-bound complex binding site; other site 504832002754 hinge residues; other site 504832002755 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_6; cd08899 504832002756 putative hydrophobic ligand binding site [chemical binding]; other site 504832002757 Protein of unknown function (DUF2945); Region: DUF2945; pfam11160 504832002758 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 504832002759 IHF dimer interface [polypeptide binding]; other site 504832002760 IHF - DNA interface [nucleotide binding]; other site 504832002761 Protein required for attachment to host cells; Region: Host_attach; pfam10116 504832002762 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 504832002763 E3 interaction surface; other site 504832002764 lipoyl attachment site [posttranslational modification]; other site 504832002765 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 504832002766 Cytochrome c; Region: Cytochrom_C; pfam00034 504832002767 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 504832002768 Ligand Binding Site [chemical binding]; other site 504832002769 NnrS protein; Region: NnrS; pfam05940 504832002770 Cytochrome c2 [Energy production and conversion]; Region: COG3474 504832002771 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 504832002772 ApbE family; Region: ApbE; pfam02424 504832002773 NosL; Region: NosL; pfam05573 504832002774 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 504832002775 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 504832002776 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 504832002777 Walker A/P-loop; other site 504832002778 ATP binding site [chemical binding]; other site 504832002779 Q-loop/lid; other site 504832002780 ABC transporter signature motif; other site 504832002781 Walker B; other site 504832002782 D-loop; other site 504832002783 H-loop/switch region; other site 504832002784 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 504832002785 nitrous-oxide reductase; Validated; Region: PRK02888 504832002786 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 504832002787 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 504832002788 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 504832002789 4Fe-4S binding domain; Region: Fer4_5; pfam12801 504832002790 4Fe-4S binding domain; Region: Fer4_5; pfam12801 504832002791 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 504832002792 dinuclear metal binding motif [ion binding]; other site 504832002793 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 504832002794 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832002795 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 504832002796 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 504832002797 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 504832002798 SCP-2 sterol transfer family; Region: SCP2; cl01225 504832002799 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 504832002800 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 504832002801 Peptidase family U32; Region: Peptidase_U32; pfam01136 504832002802 putative protease; Provisional; Region: PRK15447 504832002803 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 504832002804 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 504832002805 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 504832002806 FeS/SAM binding site; other site 504832002807 HemN C-terminal domain; Region: HemN_C; pfam06969 504832002808 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 504832002809 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 504832002810 ligand binding site [chemical binding]; other site 504832002811 flexible hinge region; other site 504832002812 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 504832002813 putative switch regulator; other site 504832002814 non-specific DNA interactions [nucleotide binding]; other site 504832002815 DNA binding site [nucleotide binding] 504832002816 sequence specific DNA binding site [nucleotide binding]; other site 504832002817 putative cAMP binding site [chemical binding]; other site 504832002818 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 504832002819 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 504832002820 putative substrate translocation pore; other site 504832002821 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 504832002822 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 504832002823 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 504832002824 [4Fe-4S] binding site [ion binding]; other site 504832002825 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 504832002826 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 504832002827 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 504832002828 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 504832002829 molybdopterin cofactor binding site; other site 504832002830 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 504832002831 4Fe-4S binding domain; Region: Fer4; cl02805 504832002832 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 504832002833 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 504832002834 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 504832002835 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 504832002836 MPT binding site; other site 504832002837 trimer interface [polypeptide binding]; other site 504832002838 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 504832002839 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 504832002840 ligand binding site [chemical binding]; other site 504832002841 flexible hinge region; other site 504832002842 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 504832002843 putative switch regulator; other site 504832002844 non-specific DNA interactions [nucleotide binding]; other site 504832002845 DNA binding site [nucleotide binding] 504832002846 sequence specific DNA binding site [nucleotide binding]; other site 504832002847 putative cAMP binding site [chemical binding]; other site 504832002848 Ketopantoate reductase [Coenzyme metabolism]; Region: ApbA; COG1893 504832002849 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832002850 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 504832002851 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 504832002852 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 504832002853 Walker A/P-loop; other site 504832002854 ATP binding site [chemical binding]; other site 504832002855 Q-loop/lid; other site 504832002856 ABC transporter signature motif; other site 504832002857 Walker B; other site 504832002858 D-loop; other site 504832002859 H-loop/switch region; other site 504832002860 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 504832002861 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 504832002862 ABC-ATPase subunit interface; other site 504832002863 dimer interface [polypeptide binding]; other site 504832002864 putative PBP binding regions; other site 504832002865 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 504832002866 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 504832002867 putative metal binding site [ion binding]; other site 504832002868 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 504832002869 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 504832002870 amidase catalytic site [active] 504832002871 Zn binding residues [ion binding]; other site 504832002872 substrate binding site [chemical binding]; other site 504832002873 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 504832002874 DNA-binding site [nucleotide binding]; DNA binding site 504832002875 RNA-binding motif; other site 504832002876 hypothetical protein; Provisional; Region: PRK05415 504832002877 Domain of unknown function (DUF697); Region: DUF697; cl12064 504832002878 YcjX-like family, DUF463; Region: DUF463; pfam04317 504832002879 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 504832002880 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 504832002881 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 504832002882 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 504832002883 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 504832002884 active site 504832002885 motif I; other site 504832002886 motif II; other site 504832002887 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 504832002888 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 504832002889 ATP-binding site [chemical binding]; other site 504832002890 Gluconate-6-phosphate binding site [chemical binding]; other site 504832002891 Shikimate kinase; Region: SKI; pfam01202 504832002892 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 504832002893 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 504832002894 putative active site [active] 504832002895 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 504832002896 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 504832002897 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 504832002898 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 504832002899 Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG1023 504832002900 bifunctional transaldolase/phosoglucose isomerase; Validated; Region: PRK09533 504832002901 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 504832002902 putative active site [active] 504832002903 catalytic residue [active] 504832002904 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 504832002905 active site 504832002906 dimer interface [polypeptide binding]; other site 504832002907 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 504832002908 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 504832002909 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 504832002910 TPP-binding site [chemical binding]; other site 504832002911 dimer interface [polypeptide binding]; other site 504832002912 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 504832002913 PYR/PP interface [polypeptide binding]; other site 504832002914 dimer interface [polypeptide binding]; other site 504832002915 TPP binding site [chemical binding]; other site 504832002916 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 504832002917 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 504832002918 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 504832002919 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 504832002920 motif II; other site 504832002921 Protein of unknown function (DUF3175); Region: DUF3175; pfam11373 504832002922 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 504832002923 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832002924 Pirin-related protein [General function prediction only]; Region: COG1741 504832002925 Pirin; Region: Pirin; pfam02678 504832002926 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832002927 transcriptional regulator; Provisional; Region: PRK10632 504832002928 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 504832002929 putative effector binding pocket; other site 504832002930 dimerization interface [polypeptide binding]; other site 504832002931 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 504832002932 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 504832002933 TPR motif; other site 504832002934 TPR repeat; Region: TPR_11; pfam13414 504832002935 binding surface 504832002936 pyruvate kinase; Provisional; Region: PRK06247 504832002937 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 504832002938 domain interfaces; other site 504832002939 active site 504832002940 Protein of unknown function (DUF1036); Region: DUF1036; pfam06282 504832002941 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3492 504832002942 hypothetical protein; Provisional; Region: PRK13694 504832002943 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 504832002944 Peptidase M15; Region: Peptidase_M15_3; cl01194 504832002945 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 504832002946 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832002947 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832002948 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 504832002949 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832002950 active site 504832002951 phosphorylation site [posttranslational modification] 504832002952 intermolecular recognition site; other site 504832002953 dimerization interface [polypeptide binding]; other site 504832002954 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 504832002955 Walker A motif; other site 504832002956 ATP binding site [chemical binding]; other site 504832002957 Walker B motif; other site 504832002958 arginine finger; other site 504832002959 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 504832002960 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 504832002961 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 504832002962 active site 504832002963 Zn binding site [ion binding]; other site 504832002964 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 504832002965 Fic/DOC family; Region: Fic; cl00960 504832002966 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 504832002967 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 504832002968 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 504832002969 ligand binding site [chemical binding]; other site 504832002970 homodimer interface [polypeptide binding]; other site 504832002971 NAD(P) binding site [chemical binding]; other site 504832002972 trimer interface B [polypeptide binding]; other site 504832002973 trimer interface A [polypeptide binding]; other site 504832002974 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 504832002975 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 504832002976 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 504832002977 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 504832002978 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832002979 PBP superfamily domain; Region: PBP_like; pfam12727 504832002980 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 504832002981 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 504832002982 NAD(P) binding site [chemical binding]; other site 504832002983 catalytic residues [active] 504832002984 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 504832002985 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 504832002986 amphipathic channel; other site 504832002987 Asn-Pro-Ala signature motifs; other site 504832002988 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 504832002989 ATP-grasp domain; Region: ATP-grasp; pfam02222 504832002990 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 504832002991 Protein of unknown function (DUF465); Region: DUF465; cl01070 504832002992 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 504832002993 hydroxyglutarate oxidase; Provisional; Region: PRK11728 504832002994 PAS domain; Region: PAS; smart00091 504832002995 PAS fold; Region: PAS_7; pfam12860 504832002996 PAS fold; Region: PAS_4; pfam08448 504832002997 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 504832002998 putative active site [active] 504832002999 heme pocket [chemical binding]; other site 504832003000 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832003001 metal binding site [ion binding]; metal-binding site 504832003002 active site 504832003003 I-site; other site 504832003004 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 504832003005 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 504832003006 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832003007 Walker A/P-loop; other site 504832003008 ATP binding site [chemical binding]; other site 504832003009 Q-loop/lid; other site 504832003010 ABC transporter signature motif; other site 504832003011 Walker B; other site 504832003012 D-loop; other site 504832003013 H-loop/switch region; other site 504832003014 TOBE domain; Region: TOBE_2; pfam08402 504832003015 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 504832003016 dimer interface [polypeptide binding]; other site 504832003017 conserved gate region; other site 504832003018 putative PBP binding loops; other site 504832003019 ABC-ATPase subunit interface; other site 504832003020 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 504832003021 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 504832003022 dimer interface [polypeptide binding]; other site 504832003023 conserved gate region; other site 504832003024 putative PBP binding loops; other site 504832003025 ABC-ATPase subunit interface; other site 504832003026 AsmA family; Region: AsmA; pfam05170 504832003027 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 504832003028 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 504832003029 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 504832003030 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 504832003031 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 504832003032 dimer interface [polypeptide binding]; other site 504832003033 conserved gate region; other site 504832003034 putative PBP binding loops; other site 504832003035 ABC-ATPase subunit interface; other site 504832003036 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 504832003037 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional; Region: PRK15046 504832003038 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 504832003039 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 504832003040 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 504832003041 putative active site [active] 504832003042 heme pocket [chemical binding]; other site 504832003043 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 504832003044 dimer interface [polypeptide binding]; other site 504832003045 phosphorylation site [posttranslational modification] 504832003046 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 504832003047 ATP binding site [chemical binding]; other site 504832003048 Mg2+ binding site [ion binding]; other site 504832003049 G-X-G motif; other site 504832003050 Phasin protein; Region: Phasin_2; cl11491 504832003051 Phasin protein; Region: Phasin_2; cl11491 504832003052 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832003053 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832003054 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 504832003055 putative effector binding pocket; other site 504832003056 dimerization interface [polypeptide binding]; other site 504832003057 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 504832003058 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832003059 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832003060 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 504832003061 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 504832003062 putative DNA binding site [nucleotide binding]; other site 504832003063 putative Zn2+ binding site [ion binding]; other site 504832003064 AsnC family; Region: AsnC_trans_reg; pfam01037 504832003065 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832003066 Predicted membrane protein [Function unknown]; Region: COG2259 504832003067 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 504832003068 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 504832003069 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 504832003070 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 504832003071 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 504832003072 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 504832003073 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 504832003074 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 504832003075 ATP-grasp domain; Region: ATP-grasp_4; cl17255 504832003076 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 504832003077 IMP binding site; other site 504832003078 dimer interface [polypeptide binding]; other site 504832003079 interdomain contacts; other site 504832003080 partial ornithine binding site; other site 504832003081 Methyltransferase domain; Region: Methyltransf_23; pfam13489 504832003082 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 504832003083 S-adenosylmethionine binding site [chemical binding]; other site 504832003084 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 504832003085 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 504832003086 dimerization interface [polypeptide binding]; other site 504832003087 DPS ferroxidase diiron center [ion binding]; other site 504832003088 ion pore; other site 504832003089 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 504832003090 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 504832003091 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 504832003092 catalytic site [active] 504832003093 subunit interface [polypeptide binding]; other site 504832003094 Yqey-like protein; Region: YqeY; pfam09424 504832003095 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; some contain an N-terminal GntR family winged HTH DNA-binding domain; Region: SRPBCC_CalC_Aha1-like_GntR-HTH; cd08893 504832003096 putative hydrophobic ligand binding site [chemical binding]; other site 504832003097 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 504832003098 dimerization interface [polypeptide binding]; other site 504832003099 putative DNA binding site [nucleotide binding]; other site 504832003100 putative Zn2+ binding site [ion binding]; other site 504832003101 N-formylglutamate amidohydrolase; Region: FGase; cl01522 504832003102 DNA primase; Validated; Region: dnaG; PRK05667 504832003103 CHC2 zinc finger; Region: zf-CHC2; pfam01807 504832003104 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 504832003105 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 504832003106 active site 504832003107 metal binding site [ion binding]; metal-binding site 504832003108 interdomain interaction site; other site 504832003109 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 504832003110 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 504832003111 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 504832003112 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 504832003113 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 504832003114 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832003115 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 504832003116 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 504832003117 DNA binding residues [nucleotide binding] 504832003118 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 504832003119 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 504832003120 gating phenylalanine in ion channel; other site 504832003121 Conserved hypothetical protein (Lin0512_fam); Region: Lin0512_fam; cl09807 504832003122 Transglycosylase SLT domain; Region: SLT_2; pfam13406 504832003123 murein hydrolase B; Provisional; Region: PRK10760; cl17906 504832003124 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 504832003125 methionine sulfoxide reductase B; Provisional; Region: PRK00222 504832003126 SelR domain; Region: SelR; pfam01641 504832003127 methionine sulfoxide reductase A; Provisional; Region: PRK13014 504832003128 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 504832003129 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832003130 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]; Region: RecD; COG0507 504832003131 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 504832003132 AAA domain; Region: AAA_30; pfam13604 504832003133 Walker A motif; other site 504832003134 ATP binding site [chemical binding]; other site 504832003135 Family description; Region: UvrD_C_2; pfam13538 504832003136 Domain of unknown function (DUF4345); Region: DUF4345; pfam14248 504832003137 Transcriptional regulator; Region: Rrf2; cl17282 504832003138 Rrf2 family protein; Region: rrf2_super; TIGR00738 504832003139 Domain of unknown function (DUF1971); Region: DUF1971; cl17717 504832003140 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 504832003141 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 504832003142 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 504832003143 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832003144 catalytic residues [active] 504832003145 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 504832003146 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 504832003147 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 504832003148 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 504832003149 molybdopterin cofactor binding site; other site 504832003150 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 504832003151 4Fe-4S binding domain; Region: Fer4; cl02805 504832003152 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 504832003153 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 504832003154 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 504832003155 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 504832003156 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 504832003157 selenocysteine synthase; Provisional; Region: PRK04311 504832003158 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 504832003159 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 504832003160 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832003161 catalytic residue [active] 504832003162 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 504832003163 Sel1-like repeats; Region: SEL1; smart00671 504832003164 Sel1-like repeats; Region: SEL1; smart00671 504832003165 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 504832003166 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 504832003167 G1 box; other site 504832003168 putative GEF interaction site [polypeptide binding]; other site 504832003169 GTP/Mg2+ binding site [chemical binding]; other site 504832003170 Switch I region; other site 504832003171 G2 box; other site 504832003172 G3 box; other site 504832003173 Switch II region; other site 504832003174 G4 box; other site 504832003175 G5 box; other site 504832003176 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 504832003177 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 504832003178 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 504832003179 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 504832003180 selenophosphate synthetase; Provisional; Region: PRK00943 504832003181 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 504832003182 dimerization interface [polypeptide binding]; other site 504832003183 putative ATP binding site [chemical binding]; other site 504832003184 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832003185 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 504832003186 putative active site [active] 504832003187 putative metal binding site [ion binding]; other site 504832003188 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 504832003189 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 504832003190 ATP binding site [chemical binding]; other site 504832003191 putative Mg++ binding site [ion binding]; other site 504832003192 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 504832003193 nucleotide binding region [chemical binding]; other site 504832003194 ATP-binding site [chemical binding]; other site 504832003195 DEAD/H associated; Region: DEAD_assoc; pfam08494 504832003196 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 504832003197 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 504832003198 ATP-dependent DNA ligase; Validated; Region: PRK09247 504832003199 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 504832003200 active site 504832003201 DNA binding site [nucleotide binding] 504832003202 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 504832003203 DNA binding site [nucleotide binding] 504832003204 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 504832003205 Fe-S cluster binding site [ion binding]; other site 504832003206 active site 504832003207 Uncharacterized conserved protein [Function unknown]; Region: COG4544 504832003208 DNA Polymerase Y-family; Region: PolY_like; cd03468 504832003209 active site 504832003210 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 504832003211 DNA binding site [nucleotide binding] 504832003212 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 504832003213 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 504832003214 putative active site [active] 504832003215 putative PHP Thumb interface [polypeptide binding]; other site 504832003216 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 504832003217 generic binding surface I; other site 504832003218 generic binding surface II; other site 504832003219 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 504832003220 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 504832003221 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 504832003222 dimerization interface [polypeptide binding]; other site 504832003223 putative DNA binding site [nucleotide binding]; other site 504832003224 putative Zn2+ binding site [ion binding]; other site 504832003225 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 504832003226 Moco binding site; other site 504832003227 metal coordination site [ion binding]; other site 504832003228 Cytochrome c; Region: Cytochrom_C; pfam00034 504832003229 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 504832003230 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 504832003231 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 504832003232 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 504832003233 Cytochrome c [Energy production and conversion]; Region: COG3258 504832003234 Cytochrome c [Energy production and conversion]; Region: COG3258 504832003235 Phosphatidylinositol-glycan biosynthesis class S protein; Region: PIG-S; pfam10510 504832003236 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 504832003237 active site 504832003238 metal binding site [ion binding]; metal-binding site 504832003239 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 504832003240 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 504832003241 DsrE/DsrF-like family; Region: DrsE; pfam02635 504832003242 DsrE/DsrF-like family; Region: DrsE; pfam02635 504832003243 Domain of unknown function (DUF336); Region: DUF336; pfam03928 504832003244 Putative transcription activator [Transcription]; Region: TenA; COG0819 504832003245 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 504832003246 Ligand Binding Site [chemical binding]; other site 504832003247 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 504832003248 Ligand Binding Site [chemical binding]; other site 504832003249 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12671 504832003250 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 504832003251 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 504832003252 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 504832003253 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 504832003254 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 504832003255 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 504832003256 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 504832003257 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 504832003258 monovalent cation:proton antiporter; Region: 2a6301s02; TIGR00943 504832003259 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 504832003260 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832003261 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832003262 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 504832003263 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 504832003264 S-adenosylmethionine binding site [chemical binding]; other site 504832003265 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 504832003266 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 504832003267 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 504832003268 Ligand Binding Site [chemical binding]; other site 504832003269 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 504832003270 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 504832003271 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 504832003272 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 504832003273 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 504832003274 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 504832003275 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 504832003276 FliG C-terminal domain; Region: FliG_C; pfam01706 504832003277 flagellar assembly protein H; Validated; Region: fliH; PRK06032 504832003278 Flagellar assembly protein FliH; Region: FliH; pfam02108 504832003279 flagellar motor switch protein; Reviewed; Region: PRK08916 504832003280 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 504832003281 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 504832003282 Walker A motif; other site 504832003283 ATP binding site [chemical binding]; other site 504832003284 Walker B motif; other site 504832003285 arginine finger; other site 504832003286 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 504832003287 oxo-acid-lyase/anthranilate synthase; Region: PLN02889 504832003288 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 504832003289 glutamine binding [chemical binding]; other site 504832003290 catalytic triad [active] 504832003291 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 504832003292 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 504832003293 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 504832003294 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 504832003295 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832003296 catalytic residue [active] 504832003297 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 504832003298 CsbD-like; Region: CsbD; pfam05532 504832003299 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 504832003300 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 504832003301 active site 504832003302 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 504832003303 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 504832003304 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 504832003305 dimer interface [polypeptide binding]; other site 504832003306 active site 504832003307 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 504832003308 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 504832003309 substrate binding site [chemical binding]; other site 504832003310 oxyanion hole (OAH) forming residues; other site 504832003311 trimer interface [polypeptide binding]; other site 504832003312 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 504832003313 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 504832003314 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 504832003315 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832003316 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 504832003317 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832003318 catalytic residue [active] 504832003319 Domain of unknown function (DUF4403); Region: DUF4403; pfam14356 504832003320 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 504832003321 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832003322 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832003323 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 504832003324 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 504832003325 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832003326 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832003327 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 504832003328 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 504832003329 putative substrate translocation pore; other site 504832003330 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 504832003331 putative substrate translocation pore; other site 504832003332 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 504832003333 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 504832003334 amidase catalytic site [active] 504832003335 Zn binding residues [ion binding]; other site 504832003336 substrate binding site [chemical binding]; other site 504832003337 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832003338 MraW methylase family; Region: Methyltransf_5; cl17771 504832003339 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 504832003340 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 504832003341 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 504832003342 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 504832003343 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 504832003344 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 504832003345 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 504832003346 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 504832003347 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 504832003348 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 504832003349 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 504832003350 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 504832003351 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 504832003352 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 504832003353 Mg++ binding site [ion binding]; other site 504832003354 putative catalytic motif [active] 504832003355 putative substrate binding site [chemical binding]; other site 504832003356 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 504832003357 GIY-YIG motif/motif A; other site 504832003358 putative active site [active] 504832003359 putative metal binding site [ion binding]; other site 504832003360 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 504832003361 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 504832003362 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 504832003363 cell division protein FtsW; Region: ftsW; TIGR02614 504832003364 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 504832003365 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 504832003366 active site 504832003367 homodimer interface [polypeptide binding]; other site 504832003368 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 504832003369 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 504832003370 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 504832003371 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 504832003372 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 504832003373 FAD binding domain; Region: FAD_binding_4; pfam01565 504832003374 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 504832003375 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 504832003376 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 504832003377 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 504832003378 ATP-grasp domain; Region: ATP-grasp_4; cl17255 504832003379 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 504832003380 Cell division protein FtsQ; Region: FtsQ; pfam03799 504832003381 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 504832003382 Cell division protein FtsA; Region: FtsA; smart00842 504832003383 Cell division protein FtsA; Region: FtsA; pfam14450 504832003384 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 504832003385 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 504832003386 nucleotide binding site [chemical binding]; other site 504832003387 SulA interaction site; other site 504832003388 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 504832003389 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 504832003390 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 504832003391 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 504832003392 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 504832003393 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 504832003394 Walker A/P-loop; other site 504832003395 ATP binding site [chemical binding]; other site 504832003396 Q-loop/lid; other site 504832003397 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 504832003398 ABC transporter signature motif; other site 504832003399 Walker B; other site 504832003400 D-loop; other site 504832003401 H-loop/switch region; other site 504832003402 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 504832003403 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 504832003404 nucleotide binding pocket [chemical binding]; other site 504832003405 K-X-D-G motif; other site 504832003406 catalytic site [active] 504832003407 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 504832003408 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 504832003409 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 504832003410 Dimer interface [polypeptide binding]; other site 504832003411 BRCT sequence motif; other site 504832003412 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 504832003413 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 504832003414 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 504832003415 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 504832003416 active site 504832003417 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 504832003418 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 504832003419 S-adenosylmethionine binding site [chemical binding]; other site 504832003420 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 504832003421 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 504832003422 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832003423 ABC-2 type transporter; Region: ABC2_membrane; cl17235 504832003424 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 504832003425 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 504832003426 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 504832003427 Walker A/P-loop; other site 504832003428 ATP binding site [chemical binding]; other site 504832003429 Q-loop/lid; other site 504832003430 ABC transporter signature motif; other site 504832003431 Walker B; other site 504832003432 D-loop; other site 504832003433 H-loop/switch region; other site 504832003434 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 504832003435 Part of AAA domain; Region: AAA_19; pfam13245 504832003436 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 504832003437 Family description; Region: UvrD_C_2; pfam13538 504832003438 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 504832003439 FAD binding domain; Region: FAD_binding_4; pfam01565 504832003440 AsmA family; Region: AsmA; pfam05170 504832003441 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 504832003442 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 504832003443 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 504832003444 fumarate hydratase; Reviewed; Region: fumC; PRK00485 504832003445 Class II fumarases; Region: Fumarase_classII; cd01362 504832003446 active site 504832003447 tetramer interface [polypeptide binding]; other site 504832003448 Stringent starvation protein B; Region: SspB; pfam04386 504832003449 thymidylate synthase; Reviewed; Region: thyA; PRK01827 504832003450 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 504832003451 dimerization interface [polypeptide binding]; other site 504832003452 active site 504832003453 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 504832003454 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 504832003455 folate binding site [chemical binding]; other site 504832003456 NADP+ binding site [chemical binding]; other site 504832003457 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 504832003458 HflK protein; Region: hflK; TIGR01933 504832003459 HflC protein; Region: hflC; TIGR01932 504832003460 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 504832003461 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 504832003462 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 504832003463 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 504832003464 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 504832003465 protein binding site [polypeptide binding]; other site 504832003466 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 504832003467 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 504832003468 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 504832003469 motif II; other site 504832003470 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 504832003471 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 504832003472 selenocysteine-specific elongation factor SelB; Region: selB; TIGR00475 504832003473 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 504832003474 G1 box; other site 504832003475 GTP/Mg2+ binding site [chemical binding]; other site 504832003476 G2 box; other site 504832003477 Switch I region; other site 504832003478 G3 box; other site 504832003479 Switch II region; other site 504832003480 G4 box; other site 504832003481 G5 box; other site 504832003482 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 504832003483 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 504832003484 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 504832003485 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 504832003486 catalytic loop [active] 504832003487 iron binding site [ion binding]; other site 504832003488 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 504832003489 4Fe-4S binding domain; Region: Fer4; pfam00037 504832003490 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 504832003491 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 504832003492 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 504832003493 putative dimer interface [polypeptide binding]; other site 504832003494 [2Fe-2S] cluster binding site [ion binding]; other site 504832003495 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 504832003496 SLBB domain; Region: SLBB; pfam10531 504832003497 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 504832003498 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 504832003499 molybdopterin cofactor binding site; other site 504832003500 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 504832003501 molybdopterin cofactor binding site; other site 504832003502 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 504832003503 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 504832003504 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 504832003505 PYR/PP interface [polypeptide binding]; other site 504832003506 dimer interface [polypeptide binding]; other site 504832003507 TPP binding site [chemical binding]; other site 504832003508 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 504832003509 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 504832003510 TPP-binding site [chemical binding]; other site 504832003511 dimer interface [polypeptide binding]; other site 504832003512 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 504832003513 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 504832003514 putative valine binding site [chemical binding]; other site 504832003515 dimer interface [polypeptide binding]; other site 504832003516 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 504832003517 ketol-acid reductoisomerase; Provisional; Region: PRK05479 504832003518 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 504832003519 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 504832003520 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 504832003521 substrate binding site [chemical binding]; other site 504832003522 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 504832003523 2-isopropylmalate synthase; Validated; Region: PRK00915 504832003524 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 504832003525 active site 504832003526 catalytic residues [active] 504832003527 metal binding site [ion binding]; metal-binding site 504832003528 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 504832003529 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 504832003530 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 504832003531 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 504832003532 DctM-like transporters; Region: DctM; pfam06808 504832003533 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 504832003534 Transcriptional regulators [Transcription]; Region: FadR; COG2186 504832003535 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832003536 DNA-binding site [nucleotide binding]; DNA binding site 504832003537 FCD domain; Region: FCD; pfam07729 504832003538 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 504832003539 FAD binding domain; Region: FAD_binding_4; pfam01565 504832003540 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832003541 Protein of unknown function (DUF2778); Region: DUF2778; pfam10908 504832003542 enterobactin exporter EntS; Provisional; Region: PRK10489 504832003543 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 504832003544 putative substrate translocation pore; other site 504832003545 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 504832003546 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 504832003547 acyl-activating enzyme (AAE) consensus motif; other site 504832003548 AMP binding site [chemical binding]; other site 504832003549 active site 504832003550 CoA binding site [chemical binding]; other site 504832003551 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 504832003552 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 504832003553 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 504832003554 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; cd00741 504832003555 nucleophilic elbow; other site 504832003556 catalytic triad; other site 504832003557 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 504832003558 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 504832003559 Cl- selectivity filter; other site 504832003560 Cl- binding residues [ion binding]; other site 504832003561 pore gating glutamate residue; other site 504832003562 dimer interface [polypeptide binding]; other site 504832003563 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 504832003564 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 504832003565 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 504832003566 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 504832003567 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 504832003568 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 504832003569 putative active site [active] 504832003570 putative substrate binding site [chemical binding]; other site 504832003571 putative cosubstrate binding site; other site 504832003572 catalytic site [active] 504832003573 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832003574 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 504832003575 S-adenosylmethionine synthetase; Validated; Region: PRK05250 504832003576 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 504832003577 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 504832003578 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 504832003579 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 504832003580 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 504832003581 homotetramer interface [polypeptide binding]; other site 504832003582 ligand binding site [chemical binding]; other site 504832003583 catalytic site [active] 504832003584 NAD binding site [chemical binding]; other site 504832003585 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 504832003586 DNA-binding site [nucleotide binding]; DNA binding site 504832003587 RNA-binding motif; other site 504832003588 Protein of unknown function, DUF606; Region: DUF606; pfam04657 504832003589 Cupin domain; Region: Cupin_2; pfam07883 504832003590 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 504832003591 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 504832003592 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 504832003593 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832003594 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832003595 Walker A/P-loop; other site 504832003596 ATP binding site [chemical binding]; other site 504832003597 Q-loop/lid; other site 504832003598 ABC transporter signature motif; other site 504832003599 Walker B; other site 504832003600 D-loop; other site 504832003601 H-loop/switch region; other site 504832003602 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 504832003603 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 504832003604 NAD binding site [chemical binding]; other site 504832003605 homodimer interface [polypeptide binding]; other site 504832003606 active site 504832003607 substrate binding site [chemical binding]; other site 504832003608 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 504832003609 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 504832003610 putative active site [active] 504832003611 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 504832003612 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 504832003613 active site 504832003614 motif I; other site 504832003615 motif II; other site 504832003616 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 504832003617 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 504832003618 dimer interface [polypeptide binding]; other site 504832003619 active site 504832003620 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 504832003621 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 504832003622 putative active site [active] 504832003623 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 504832003624 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 504832003625 NADP binding site [chemical binding]; other site 504832003626 homopentamer interface [polypeptide binding]; other site 504832003627 substrate binding site [chemical binding]; other site 504832003628 active site 504832003629 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 504832003630 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 504832003631 putative ribose interaction site [chemical binding]; other site 504832003632 putative ADP binding site [chemical binding]; other site 504832003633 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 504832003634 active site 504832003635 nucleotide binding site [chemical binding]; other site 504832003636 HIGH motif; other site 504832003637 KMSKS motif; other site 504832003638 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 504832003639 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 504832003640 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 504832003641 putative NAD(P) binding site [chemical binding]; other site 504832003642 active site 504832003643 putative substrate binding site [chemical binding]; other site 504832003644 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 504832003645 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 504832003646 Substrate binding site; other site 504832003647 Cupin domain; Region: Cupin_2; cl17218 504832003648 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 504832003649 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 504832003650 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 504832003651 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 504832003652 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 504832003653 inhibitor-cofactor binding pocket; inhibition site 504832003654 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832003655 catalytic residue [active] 504832003656 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 504832003657 MviN-like protein; Region: MVIN; pfam03023 504832003658 CHRD domain; Region: CHRD; pfam07452 504832003659 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 504832003660 dimer interface [polypeptide binding]; other site 504832003661 substrate binding site [chemical binding]; other site 504832003662 ATP binding site [chemical binding]; other site 504832003663 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 504832003664 S-adenosylmethionine binding site [chemical binding]; other site 504832003665 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832003666 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 504832003667 putative active site [active] 504832003668 putative metal binding site [ion binding]; other site 504832003669 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832003670 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 504832003671 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 504832003672 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 504832003673 tetramer interface [polypeptide binding]; other site 504832003674 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832003675 catalytic residue [active] 504832003676 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 504832003677 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 504832003678 active site 504832003679 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 504832003680 anti sigma factor interaction site; other site 504832003681 regulatory phosphorylation site [posttranslational modification]; other site 504832003682 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 504832003683 Permease; Region: Permease; pfam02405 504832003684 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 504832003685 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 504832003686 Walker A/P-loop; other site 504832003687 ATP binding site [chemical binding]; other site 504832003688 Q-loop/lid; other site 504832003689 ABC transporter signature motif; other site 504832003690 Walker B; other site 504832003691 D-loop; other site 504832003692 H-loop/switch region; other site 504832003693 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 504832003694 mce related protein; Region: MCE; pfam02470 504832003695 Glucokinase; Region: Glucokinase; cl17310 504832003696 glucokinase, proteobacterial type; Region: glk; TIGR00749 504832003697 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 504832003698 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 504832003699 putative binding surface; other site 504832003700 active site 504832003701 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 504832003702 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 504832003703 catalytic loop [active] 504832003704 iron binding site [ion binding]; other site 504832003705 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 504832003706 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832003707 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832003708 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 504832003709 oxyanion hole [active] 504832003710 Predicted integral membrane protein [Function unknown]; Region: COG0392 504832003711 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 504832003712 dimerization interface [polypeptide binding]; other site 504832003713 metal binding site [ion binding]; metal-binding site 504832003714 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 504832003715 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 504832003716 non-specific DNA binding site [nucleotide binding]; other site 504832003717 salt bridge; other site 504832003718 sequence-specific DNA binding site [nucleotide binding]; other site 504832003719 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 504832003720 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 504832003721 catalytic core [active] 504832003722 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 504832003723 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 504832003724 methionine sulfoxide reductase B; Provisional; Region: PRK00222 504832003725 SelR domain; Region: SelR; pfam01641 504832003726 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 504832003727 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 504832003728 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 504832003729 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 504832003730 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 504832003731 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 504832003732 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08913 504832003733 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 504832003734 flagellar biosynthesis repressor FlbT; Reviewed; Region: flbT; PRK12791 504832003735 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 504832003736 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 504832003737 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 504832003738 TPR repeat; Region: TPR_11; pfam13414 504832003739 binding surface 504832003740 TPR motif; other site 504832003741 TPR repeat; Region: TPR_11; pfam13414 504832003742 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 504832003743 binding surface 504832003744 TPR motif; other site 504832003745 TPR repeat; Region: TPR_11; pfam13414 504832003746 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 504832003747 binding surface 504832003748 TPR motif; other site 504832003749 TPR repeat; Region: TPR_11; pfam13414 504832003750 flagellar biosynthesis regulatory protein FlaF; Reviewed; Region: flaF; PRK12794 504832003751 chemotactic signal-response protein CheL; Provisional; Region: PRK12790 504832003752 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 504832003753 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 504832003754 flagellar assembly regulator FliX; Reviewed; Region: fliX; PRK12787 504832003755 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 504832003756 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 504832003757 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 504832003758 SAF-like; Region: SAF_2; pfam13144 504832003759 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 504832003760 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 504832003761 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 504832003762 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 504832003763 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12689 504832003764 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 504832003765 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 504832003766 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK12785 504832003767 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 504832003768 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 504832003769 Uncharacterized conserved protein [Function unknown]; Region: COG3334 504832003770 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 504832003771 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 504832003772 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 504832003773 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 504832003774 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 504832003775 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00732 504832003776 flagellar biosynthesis protein FliQ; Reviewed; Region: fliQ; PRK06010 504832003777 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 504832003778 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 504832003779 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 504832003780 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 504832003781 PAS domain; Region: PAS_9; pfam13426 504832003782 putative active site [active] 504832003783 heme pocket [chemical binding]; other site 504832003784 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 504832003785 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 504832003786 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 504832003787 putative active site [active] 504832003788 heme pocket [chemical binding]; other site 504832003789 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 504832003790 dimer interface [polypeptide binding]; other site 504832003791 phosphorylation site [posttranslational modification] 504832003792 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 504832003793 ATP binding site [chemical binding]; other site 504832003794 Mg2+ binding site [ion binding]; other site 504832003795 G-X-G motif; other site 504832003796 Response regulator receiver domain; Region: Response_reg; pfam00072 504832003797 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832003798 active site 504832003799 phosphorylation site [posttranslational modification] 504832003800 intermolecular recognition site; other site 504832003801 dimerization interface [polypeptide binding]; other site 504832003802 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 504832003803 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 504832003804 glutathione s-transferase; Provisional; Region: PTZ00057 504832003805 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 504832003806 dimer interface [polypeptide binding]; other site 504832003807 N-terminal domain interface [polypeptide binding]; other site 504832003808 substrate binding pocket (H-site) [chemical binding]; other site 504832003809 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 504832003810 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 504832003811 dimer interface [polypeptide binding]; other site 504832003812 fumarate hydratase; Provisional; Region: PRK15389 504832003813 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 504832003814 Fumarase C-terminus; Region: Fumerase_C; pfam05683 504832003815 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 504832003816 putative C-terminal domain interface [polypeptide binding]; other site 504832003817 putative GSH binding site (G-site) [chemical binding]; other site 504832003818 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832003819 putative dimer interface [polypeptide binding]; other site 504832003820 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 504832003821 dimer interface [polypeptide binding]; other site 504832003822 N-terminal domain interface [polypeptide binding]; other site 504832003823 putative substrate binding pocket (H-site) [chemical binding]; other site 504832003824 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 504832003825 dimerization interface [polypeptide binding]; other site 504832003826 putative DNA binding site [nucleotide binding]; other site 504832003827 putative Zn2+ binding site [ion binding]; other site 504832003828 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 504832003829 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832003830 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 504832003831 dimer interface [polypeptide binding]; other site 504832003832 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 504832003833 putative hydrophobic ligand binding site [chemical binding]; other site 504832003834 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 504832003835 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 504832003836 putative substrate translocation pore; other site 504832003837 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 504832003838 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 504832003839 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 504832003840 catalytic residues [active] 504832003841 Cupin-like domain; Region: Cupin_8; pfam13621 504832003842 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 504832003843 LTXXQ motif family protein; Region: LTXXQ; pfam07813 504832003844 LTXXQ motif family protein; Region: LTXXQ; pfam07813 504832003845 Flp/Fap pilin component; Region: Flp_Fap; pfam04964 504832003846 camphor resistance protein CrcB; Provisional; Region: PRK14195 504832003847 hypothetical protein; Provisional; Region: PRK02237 504832003848 recombinase A; Provisional; Region: recA; PRK09354 504832003849 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 504832003850 hexamer interface [polypeptide binding]; other site 504832003851 Walker A motif; other site 504832003852 ATP binding site [chemical binding]; other site 504832003853 Walker B motif; other site 504832003854 glycine dehydrogenase; Provisional; Region: PRK05367 504832003855 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 504832003856 tetramer interface [polypeptide binding]; other site 504832003857 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832003858 catalytic residue [active] 504832003859 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 504832003860 tetramer interface [polypeptide binding]; other site 504832003861 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832003862 catalytic residue [active] 504832003863 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 504832003864 lipoyl attachment site [posttranslational modification]; other site 504832003865 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 504832003866 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 504832003867 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 504832003868 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 504832003869 motif 1; other site 504832003870 active site 504832003871 motif 2; other site 504832003872 motif 3; other site 504832003873 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 504832003874 DHHA1 domain; Region: DHHA1; pfam02272 504832003875 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 504832003876 Ligand Binding Site [chemical binding]; other site 504832003877 putative cation:proton antiport protein; Provisional; Region: PRK10669 504832003878 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 504832003879 TrkA-N domain; Region: TrkA_N; pfam02254 504832003880 isocitrate dehydrogenase; Validated; Region: PRK08299 504832003881 Hantavirus nucleocapsid protein; Region: Hanta_nucleocap; pfam00846 504832003882 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 504832003883 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 504832003884 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 504832003885 putative active site [active] 504832003886 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832003887 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 504832003888 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 504832003889 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 504832003890 ATP binding site [chemical binding]; other site 504832003891 active site 504832003892 substrate binding site [chemical binding]; other site 504832003893 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed; Region: PRK05974 504832003894 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 504832003895 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 504832003896 putative active site [active] 504832003897 catalytic triad [active] 504832003898 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 504832003899 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 504832003900 dimerization interface [polypeptide binding]; other site 504832003901 ATP binding site [chemical binding]; other site 504832003902 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 504832003903 dimerization interface [polypeptide binding]; other site 504832003904 ATP binding site [chemical binding]; other site 504832003905 Acyltransferase family; Region: Acyl_transf_3; pfam01757 504832003906 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 504832003907 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 504832003908 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 504832003909 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 504832003910 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 504832003911 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 504832003912 putative GSH binding site [chemical binding]; other site 504832003913 catalytic residues [active] 504832003914 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 504832003915 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 504832003916 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 504832003917 RNA binding surface [nucleotide binding]; other site 504832003918 glutamate racemase; Provisional; Region: PRK00865 504832003919 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 504832003920 Serine hydrolase; Region: Ser_hydrolase; pfam06821 504832003921 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 504832003922 adenylosuccinate lyase; Provisional; Region: PRK07492 504832003923 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 504832003924 tetramer interface [polypeptide binding]; other site 504832003925 active site 504832003926 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 504832003927 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 504832003928 substrate binding site [chemical binding]; other site 504832003929 hexamer interface [polypeptide binding]; other site 504832003930 metal binding site [ion binding]; metal-binding site 504832003931 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 504832003932 EF-hand domain pair; Region: EF_hand_5; pfam13499 504832003933 Ca2+ binding site [ion binding]; other site 504832003934 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 504832003935 KTSC domain; Region: KTSC; pfam13619 504832003936 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 504832003937 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832003938 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 504832003939 Cytochrome c; Region: Cytochrom_C; pfam00034 504832003940 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 504832003941 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832003942 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 504832003943 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 504832003944 TPR motif; other site 504832003945 binding surface 504832003946 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 504832003947 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 504832003948 cleavage site 504832003949 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 504832003950 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 504832003951 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 504832003952 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 504832003953 dimerization interface [polypeptide binding]; other site 504832003954 ligand binding site [chemical binding]; other site 504832003955 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832003956 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832003957 Walker A/P-loop; other site 504832003958 ATP binding site [chemical binding]; other site 504832003959 Q-loop/lid; other site 504832003960 ABC transporter signature motif; other site 504832003961 Walker B; other site 504832003962 D-loop; other site 504832003963 H-loop/switch region; other site 504832003964 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832003965 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832003966 Walker A/P-loop; other site 504832003967 ATP binding site [chemical binding]; other site 504832003968 Q-loop/lid; other site 504832003969 ABC transporter signature motif; other site 504832003970 Walker B; other site 504832003971 D-loop; other site 504832003972 H-loop/switch region; other site 504832003973 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 504832003974 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 504832003975 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 504832003976 TM-ABC transporter signature motif; other site 504832003977 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 504832003978 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 504832003979 TM-ABC transporter signature motif; other site 504832003980 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 504832003981 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 504832003982 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 504832003983 XdhC Rossmann domain; Region: XdhC_C; pfam13478 504832003984 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 504832003985 putative MPT binding site; other site 504832003986 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 504832003987 Ligand binding site; other site 504832003988 metal-binding site 504832003989 Domain of unknown function (DUF4189); Region: DUF4189; pfam13827 504832003990 Protein of unknown function, DUF488; Region: DUF488; pfam04343 504832003991 Protein of unknown function DUF72; Region: DUF72; pfam01904 504832003992 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 504832003993 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 504832003994 Ligand binding site; other site 504832003995 Putative Catalytic site; other site 504832003996 DXD motif; other site 504832003997 Predicted membrane protein [Function unknown]; Region: COG2246 504832003998 GtrA-like protein; Region: GtrA; pfam04138 504832003999 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 504832004000 Uncharacterized conserved protein [Function unknown]; Region: COG2128 504832004001 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 504832004002 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 504832004003 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 504832004004 substrate binding pocket [chemical binding]; other site 504832004005 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 504832004006 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 504832004007 membrane-bound complex binding site; other site 504832004008 hinge residues; other site 504832004009 MarR family; Region: MarR_2; cl17246 504832004010 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 504832004011 sequence-specific DNA binding site [nucleotide binding]; other site 504832004012 CHAT domain; Region: CHAT; cl17868 504832004013 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 504832004014 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 504832004015 ring oligomerisation interface [polypeptide binding]; other site 504832004016 ATP/Mg binding site [chemical binding]; other site 504832004017 stacking interactions; other site 504832004018 hinge regions; other site 504832004019 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 504832004020 oligomerisation interface [polypeptide binding]; other site 504832004021 mobile loop; other site 504832004022 roof hairpin; other site 504832004023 Usg-like family; Region: Usg; pfam06233 504832004024 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 504832004025 classical (c) SDRs; Region: SDR_c; cd05233 504832004026 NAD(P) binding site [chemical binding]; other site 504832004027 active site 504832004028 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 504832004029 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 504832004030 active site 504832004031 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 504832004032 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 504832004033 putative MPT binding site; other site 504832004034 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832004035 active site 504832004036 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 504832004037 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 504832004038 putative NAD(P) binding site [chemical binding]; other site 504832004039 putative substrate binding site [chemical binding]; other site 504832004040 catalytic Zn binding site [ion binding]; other site 504832004041 structural Zn binding site [ion binding]; other site 504832004042 dimer interface [polypeptide binding]; other site 504832004043 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 504832004044 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 504832004045 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 504832004046 salicylate hydroxylase; Provisional; Region: PRK08163 504832004047 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 504832004048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 504832004049 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 504832004050 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 504832004051 serine acetyltransferase; Provisional; Region: cysE; PRK11132 504832004052 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 504832004053 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 504832004054 trimer interface [polypeptide binding]; other site 504832004055 active site 504832004056 substrate binding site [chemical binding]; other site 504832004057 CoA binding site [chemical binding]; other site 504832004058 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 504832004059 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 504832004060 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 504832004061 trimer interface [polypeptide binding]; other site 504832004062 putative metal binding site [ion binding]; other site 504832004063 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 504832004064 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 504832004065 putative active site [active] 504832004066 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; pfam06035 504832004067 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 504832004068 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 504832004069 active site 504832004070 oxyanion hole [active] 504832004071 catalytic triad [active] 504832004072 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]; Region: COG2191 504832004073 PilZ domain; Region: PilZ; pfam07238 504832004074 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 504832004075 DNA binding site [nucleotide binding] 504832004076 Int/Topo IB signature motif; other site 504832004077 active site 504832004078 catalytic residues [active] 504832004079 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 504832004080 Domain of unknown function (DUF4326); Region: DUF4326; pfam14216 504832004081 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 504832004082 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 504832004083 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 504832004084 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 504832004085 dimer interface [polypeptide binding]; other site 504832004086 ssDNA binding site [nucleotide binding]; other site 504832004087 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832004088 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 504832004089 RNA/DNA hybrid binding site [nucleotide binding]; other site 504832004090 active site 504832004091 RecT family; Region: RecT; pfam03837 504832004092 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 504832004093 GcrA cell cycle regulator; Region: GcrA; cl11564 504832004094 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; cl17280 504832004095 DNA methylase; Region: N6_N4_Mtase; cl17433 504832004096 Replicative DNA helicase [DNA replication, recombination, and repair]; Region: DnaB; COG0305 504832004097 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 504832004098 AAA domain; Region: AAA_25; pfam13481 504832004099 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 504832004100 ATP binding site [chemical binding]; other site 504832004101 Walker A motif; other site 504832004102 Walker B motif; other site 504832004103 Domain of unknown function DUF87; Region: DUF87; pfam01935 504832004104 HerA helicase [Replication, recombination, and repair]; Region: COG0433 504832004105 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 504832004106 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 504832004107 cofactor binding site; other site 504832004108 DNA binding site [nucleotide binding] 504832004109 substrate interaction site [chemical binding]; other site 504832004110 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 504832004111 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 504832004112 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 504832004113 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 504832004114 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 504832004115 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 504832004116 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 504832004117 tandem repeat interface [polypeptide binding]; other site 504832004118 oligomer interface [polypeptide binding]; other site 504832004119 active site residues [active] 504832004120 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 504832004121 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 504832004122 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 504832004123 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 504832004124 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 504832004125 Baseplate J-like protein; Region: Baseplate_J; cl01294 504832004126 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 504832004127 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 504832004128 Phage tail tube protein FII; Region: Phage_tube; cl01390 504832004129 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 504832004130 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 504832004131 Phage Tail Protein X; Region: Phage_tail_X; cl02088 504832004132 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 504832004133 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 504832004134 TIGR02594 family protein; Region: TIGR02594 504832004135 PAS domain; Region: PAS_5; pfam07310 504832004136 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 504832004137 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 504832004138 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 504832004139 FOG: CBS domain [General function prediction only]; Region: COG0517 504832004140 hypothetical protein; Provisional; Region: PRK10279 504832004141 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 504832004142 nucleophile elbow; other site 504832004143 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 504832004144 putative FMN binding site [chemical binding]; other site 504832004145 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 504832004146 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 504832004147 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 504832004148 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 504832004149 active site 504832004150 dimer interface [polypeptide binding]; other site 504832004151 motif 1; other site 504832004152 motif 2; other site 504832004153 motif 3; other site 504832004154 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 504832004155 anticodon binding site; other site 504832004156 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 504832004157 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 504832004158 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 504832004159 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 504832004160 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 504832004161 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 504832004162 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 504832004163 catalytic loop [active] 504832004164 iron binding site [ion binding]; other site 504832004165 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 504832004166 hypothetical protein; Validated; Region: PRK00041 504832004167 Predicted periplasmic protein [Function unknown]; Region: COG3904 504832004168 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 504832004169 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 504832004170 trimerization site [polypeptide binding]; other site 504832004171 active site 504832004172 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 504832004173 GTP cyclohydrolase I; Provisional; Region: PLN03044 504832004174 active site 504832004175 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 504832004176 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 504832004177 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832004178 catalytic residue [active] 504832004179 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 504832004180 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 504832004181 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 504832004182 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832004183 active site 504832004184 phosphorylation site [posttranslational modification] 504832004185 intermolecular recognition site; other site 504832004186 dimerization interface [polypeptide binding]; other site 504832004187 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 504832004188 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 504832004189 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 504832004190 N-terminal plug; other site 504832004191 ligand-binding site [chemical binding]; other site 504832004192 TspO/MBR family; Region: TspO_MBR; pfam03073 504832004193 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 504832004194 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 504832004195 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 504832004196 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 504832004197 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 504832004198 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832004199 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 504832004200 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832004201 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 504832004202 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 504832004203 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 504832004204 metal ion-dependent adhesion site (MIDAS); other site 504832004205 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 504832004206 substrate binding site [chemical binding]; other site 504832004207 Predicted aconitase [General function prediction only]; Region: COG1679 504832004208 Protein of unknown function (DUF521); Region: DUF521; pfam04412 504832004209 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 504832004210 NMT1-like family; Region: NMT1_2; pfam13379 504832004211 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832004212 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 504832004213 dimer interface [polypeptide binding]; other site 504832004214 conserved gate region; other site 504832004215 putative PBP binding loops; other site 504832004216 ABC-ATPase subunit interface; other site 504832004217 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832004218 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832004219 Walker A/P-loop; other site 504832004220 ATP binding site [chemical binding]; other site 504832004221 Q-loop/lid; other site 504832004222 ABC transporter signature motif; other site 504832004223 Walker B; other site 504832004224 D-loop; other site 504832004225 H-loop/switch region; other site 504832004226 chaperonin_like superfamily. 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. There are 2 main chaperonin groups. The symmetry of type I...; Region: chaperonin_like; cl02777 504832004227 thermosome, various subunits, archaeal; Region: thermosome_arch; TIGR02339 504832004228 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 504832004229 HAMP domain; Region: HAMP; pfam00672 504832004230 dimerization interface [polypeptide binding]; other site 504832004231 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 504832004232 HWE histidine kinase; Region: HWE_HK; pfam07536 504832004233 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832004234 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 504832004235 active site 504832004236 metal binding site [ion binding]; metal-binding site 504832004237 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 504832004238 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 504832004239 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 504832004240 putative homodimer interface [polypeptide binding]; other site 504832004241 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 504832004242 heterodimer interface [polypeptide binding]; other site 504832004243 homodimer interface [polypeptide binding]; other site 504832004244 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 504832004245 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 504832004246 23S rRNA interface [nucleotide binding]; other site 504832004247 L7/L12 interface [polypeptide binding]; other site 504832004248 putative thiostrepton binding site; other site 504832004249 L25 interface [polypeptide binding]; other site 504832004250 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 504832004251 mRNA/rRNA interface [nucleotide binding]; other site 504832004252 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 504832004253 23S rRNA interface [nucleotide binding]; other site 504832004254 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 504832004255 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 504832004256 core dimer interface [polypeptide binding]; other site 504832004257 peripheral dimer interface [polypeptide binding]; other site 504832004258 L10 interface [polypeptide binding]; other site 504832004259 L11 interface [polypeptide binding]; other site 504832004260 putative EF-Tu interaction site [polypeptide binding]; other site 504832004261 putative EF-G interaction site [polypeptide binding]; other site 504832004262 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 504832004263 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 504832004264 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 504832004265 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 504832004266 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 504832004267 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 504832004268 RPB3 interaction site [polypeptide binding]; other site 504832004269 RPB1 interaction site [polypeptide binding]; other site 504832004270 RPB11 interaction site [polypeptide binding]; other site 504832004271 RPB10 interaction site [polypeptide binding]; other site 504832004272 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 504832004273 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 504832004274 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 504832004275 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 504832004276 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 504832004277 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 504832004278 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 504832004279 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 504832004280 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 504832004281 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 504832004282 DNA binding site [nucleotide binding] 504832004283 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 504832004284 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832004285 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 504832004286 Methyltransferase domain; Region: Methyltransf_11; pfam08241 504832004287 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 504832004288 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832004289 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832004290 Walker A/P-loop; other site 504832004291 ATP binding site [chemical binding]; other site 504832004292 Q-loop/lid; other site 504832004293 ABC transporter signature motif; other site 504832004294 Walker B; other site 504832004295 D-loop; other site 504832004296 H-loop/switch region; other site 504832004297 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 504832004298 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 504832004299 active site 504832004300 Predicted ATP-grasp enzyme [General function prediction only]; Region: COG3919 504832004301 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 504832004302 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 504832004303 S17 interaction site [polypeptide binding]; other site 504832004304 S8 interaction site; other site 504832004305 16S rRNA interaction site [nucleotide binding]; other site 504832004306 streptomycin interaction site [chemical binding]; other site 504832004307 23S rRNA interaction site [nucleotide binding]; other site 504832004308 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 504832004309 30S ribosomal protein S7; Validated; Region: PRK05302 504832004310 elongation factor G; Reviewed; Region: PRK00007 504832004311 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 504832004312 G1 box; other site 504832004313 putative GEF interaction site [polypeptide binding]; other site 504832004314 GTP/Mg2+ binding site [chemical binding]; other site 504832004315 Switch I region; other site 504832004316 G2 box; other site 504832004317 G3 box; other site 504832004318 Switch II region; other site 504832004319 G4 box; other site 504832004320 G5 box; other site 504832004321 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 504832004322 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 504832004323 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 504832004324 elongation factor Tu; Reviewed; Region: PRK00049 504832004325 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 504832004326 G1 box; other site 504832004327 GEF interaction site [polypeptide binding]; other site 504832004328 GTP/Mg2+ binding site [chemical binding]; other site 504832004329 Switch I region; other site 504832004330 G2 box; other site 504832004331 G3 box; other site 504832004332 Switch II region; other site 504832004333 G4 box; other site 504832004334 G5 box; other site 504832004335 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 504832004336 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 504832004337 Antibiotic Binding Site [chemical binding]; other site 504832004338 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 504832004339 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 504832004340 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 504832004341 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 504832004342 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 504832004343 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 504832004344 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 504832004345 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 504832004346 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 504832004347 putative translocon binding site; other site 504832004348 protein-rRNA interface [nucleotide binding]; other site 504832004349 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 504832004350 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 504832004351 G-X-X-G motif; other site 504832004352 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 504832004353 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 504832004354 23S rRNA interface [nucleotide binding]; other site 504832004355 5S rRNA interface [nucleotide binding]; other site 504832004356 putative antibiotic binding site [chemical binding]; other site 504832004357 L25 interface [polypeptide binding]; other site 504832004358 L27 interface [polypeptide binding]; other site 504832004359 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 504832004360 putative translocon interaction site; other site 504832004361 23S rRNA interface [nucleotide binding]; other site 504832004362 signal recognition particle (SRP54) interaction site; other site 504832004363 L23 interface [polypeptide binding]; other site 504832004364 trigger factor interaction site; other site 504832004365 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 504832004366 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 504832004367 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 504832004368 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 504832004369 RNA binding site [nucleotide binding]; other site 504832004370 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 504832004371 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 504832004372 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 504832004373 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 504832004374 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 504832004375 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 504832004376 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 504832004377 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 504832004378 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 504832004379 5S rRNA interface [nucleotide binding]; other site 504832004380 23S rRNA interface [nucleotide binding]; other site 504832004381 L5 interface [polypeptide binding]; other site 504832004382 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 504832004383 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 504832004384 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 504832004385 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 504832004386 23S rRNA binding site [nucleotide binding]; other site 504832004387 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 504832004388 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 504832004389 SecY translocase; Region: SecY; pfam00344 504832004390 adenylate kinase; Reviewed; Region: adk; PRK00279 504832004391 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 504832004392 AMP-binding site [chemical binding]; other site 504832004393 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 504832004394 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 504832004395 30S ribosomal protein S13; Region: bact_S13; TIGR03631 504832004396 30S ribosomal protein S11; Validated; Region: PRK05309 504832004397 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 504832004398 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 504832004399 alphaNTD - beta interaction site [polypeptide binding]; other site 504832004400 alphaNTD homodimer interface [polypeptide binding]; other site 504832004401 alphaNTD - beta' interaction site [polypeptide binding]; other site 504832004402 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 504832004403 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 504832004404 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 504832004405 Ankyrin repeat; Region: Ank; pfam00023 504832004406 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 504832004407 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 504832004408 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 504832004409 classical (c) SDRs; Region: SDR_c; cd05233 504832004410 NAD(P) binding site [chemical binding]; other site 504832004411 active site 504832004412 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 504832004413 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 504832004414 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 504832004415 putative NAD(P) binding site [chemical binding]; other site 504832004416 dimer interface [polypeptide binding]; other site 504832004417 Predicted transcriptional regulators [Transcription]; Region: COG1733 504832004418 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 504832004419 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 504832004420 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 504832004421 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 504832004422 protein binding site [polypeptide binding]; other site 504832004423 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 504832004424 protein binding site [polypeptide binding]; other site 504832004425 recombination factor protein RarA; Reviewed; Region: PRK13342 504832004426 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 504832004427 Walker A motif; other site 504832004428 ATP binding site [chemical binding]; other site 504832004429 Walker B motif; other site 504832004430 arginine finger; other site 504832004431 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 504832004432 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 504832004433 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 504832004434 RNA binding surface [nucleotide binding]; other site 504832004435 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 504832004436 active site 504832004437 ATP12 chaperone protein; Region: ATP12; cl02228 504832004438 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 504832004439 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 504832004440 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 504832004441 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 504832004442 tetramer interface [polypeptide binding]; other site 504832004443 active site 504832004444 Mg2+/Mn2+ binding site [ion binding]; other site 504832004445 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 504832004446 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 504832004447 inhibitor site; inhibition site 504832004448 active site 504832004449 dimer interface [polypeptide binding]; other site 504832004450 catalytic residue [active] 504832004451 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 504832004452 atypical (a) SDRs, subgroup 6; Region: SDR_a6; cd05267 504832004453 NADH(P)-binding; Region: NAD_binding_10; pfam13460 504832004454 putative NAD(P) binding site [chemical binding]; other site 504832004455 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 504832004456 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 504832004457 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 504832004458 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832004459 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832004460 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 504832004461 putative effector binding pocket; other site 504832004462 putative dimerization interface [polypeptide binding]; other site 504832004463 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 504832004464 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 504832004465 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 504832004466 cyclase homology domain; Region: CHD; cd07302 504832004467 nucleotidyl binding site; other site 504832004468 metal binding site [ion binding]; metal-binding site 504832004469 dimer interface [polypeptide binding]; other site 504832004470 PilZ domain; Region: PilZ; pfam07238 504832004471 Predicted periplasmic protein [Function unknown]; Region: COG3904 504832004472 Transcriptional regulators [Transcription]; Region: MarR; COG1846 504832004473 MarR family; Region: MarR; pfam01047 504832004474 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 504832004475 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 504832004476 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 504832004477 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 504832004478 substrate binding site [chemical binding]; other site 504832004479 catalytic Zn binding site [ion binding]; other site 504832004480 NAD binding site [chemical binding]; other site 504832004481 structural Zn binding site [ion binding]; other site 504832004482 dimer interface [polypeptide binding]; other site 504832004483 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 504832004484 EamA-like transporter family; Region: EamA; pfam00892 504832004485 EamA-like transporter family; Region: EamA; pfam00892 504832004486 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 504832004487 DNA photolyase; Region: DNA_photolyase; pfam00875 504832004488 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 504832004489 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 504832004490 dimer interface [polypeptide binding]; other site 504832004491 decamer (pentamer of dimers) interface [polypeptide binding]; other site 504832004492 catalytic triad [active] 504832004493 Acylphosphatases [Energy production and conversion]; Region: AcyP; COG1254 504832004494 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 504832004495 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 504832004496 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832004497 lipoate-protein ligase B; Provisional; Region: PRK14341 504832004498 hypothetical protein; Validated; Region: PRK06033 504832004499 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 504832004500 MOSC domain; Region: MOSC; pfam03473 504832004501 3-alpha domain; Region: 3-alpha; pfam03475 504832004502 Dodecin; Region: Dodecin; pfam07311 504832004503 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 504832004504 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 504832004505 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 504832004506 Zn binding residues [ion binding]; other site 504832004507 substrate binding site [chemical binding]; other site 504832004508 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 504832004509 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 504832004510 NodB motif; other site 504832004511 active site 504832004512 catalytic site [active] 504832004513 metal binding site [ion binding]; metal-binding site 504832004514 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 504832004515 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 504832004516 NodB motif; other site 504832004517 active site 504832004518 catalytic site [active] 504832004519 metal binding site [ion binding]; metal-binding site 504832004520 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 504832004521 non-specific DNA binding site [nucleotide binding]; other site 504832004522 salt bridge; other site 504832004523 sequence-specific DNA binding site [nucleotide binding]; other site 504832004524 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 504832004525 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 504832004526 active site 504832004527 catalytic tetrad [active] 504832004528 Uncharacterized conserved protein [Function unknown]; Region: COG1434 504832004529 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 504832004530 putative active site [active] 504832004531 Protein of unknown function (DUF3253); Region: DUF3253; pfam11625 504832004532 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832004533 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 504832004534 putative C-terminal domain interface [polypeptide binding]; other site 504832004535 putative GSH binding site (G-site) [chemical binding]; other site 504832004536 putative dimer interface [polypeptide binding]; other site 504832004537 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 504832004538 putative N-terminal domain interface [polypeptide binding]; other site 504832004539 putative dimer interface [polypeptide binding]; other site 504832004540 putative substrate binding pocket (H-site) [chemical binding]; other site 504832004541 Histidine kinase N terminal; Region: HisK_N; pfam09385 504832004542 Protein of unknown function (DUF1489); Region: DUF1489; pfam07370 504832004543 Pantoate-beta-alanine ligase; Region: PanC; cd00560 504832004544 pantoate--beta-alanine ligase; Region: panC; TIGR00018 504832004545 active site 504832004546 ATP-binding site [chemical binding]; other site 504832004547 pantoate-binding site; other site 504832004548 HXXH motif; other site 504832004549 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 504832004550 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 504832004551 nucleophilic elbow; other site 504832004552 catalytic triad; other site 504832004553 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 504832004554 HSP70 interaction site [polypeptide binding]; other site 504832004555 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 504832004556 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 504832004557 Sporulation related domain; Region: SPOR; pfam05036 504832004558 Phasin protein; Region: Phasin_2; pfam09361 504832004559 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 504832004560 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 504832004561 Uncharacterized conserved protein [Function unknown]; Region: COG2127 504832004562 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 504832004563 Clp amino terminal domain; Region: Clp_N; pfam02861 504832004564 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 504832004565 Walker A motif; other site 504832004566 ATP binding site [chemical binding]; other site 504832004567 Walker B motif; other site 504832004568 arginine finger; other site 504832004569 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 504832004570 Walker A motif; other site 504832004571 ATP binding site [chemical binding]; other site 504832004572 Walker B motif; other site 504832004573 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 504832004574 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832004575 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 504832004576 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832004577 catalytic residue [active] 504832004578 Sporulation related domain; Region: SPOR; pfam05036 504832004579 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 504832004580 Protein of unknown function, DUF482; Region: DUF482; pfam04339 504832004581 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 504832004582 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 504832004583 active site 504832004584 catalytic site [active] 504832004585 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 504832004586 homotrimer interaction site [polypeptide binding]; other site 504832004587 putative active site [active] 504832004588 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 504832004589 DNA polymerase IV; Provisional; Region: PRK02794 504832004590 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 504832004591 active site 504832004592 DNA binding site [nucleotide binding] 504832004593 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 504832004594 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 504832004595 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832004596 active site 504832004597 phosphorylation site [posttranslational modification] 504832004598 intermolecular recognition site; other site 504832004599 dimerization interface [polypeptide binding]; other site 504832004600 response regulator PleD; Reviewed; Region: pleD; PRK09581 504832004601 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832004602 active site 504832004603 phosphorylation site [posttranslational modification] 504832004604 intermolecular recognition site; other site 504832004605 dimerization interface [polypeptide binding]; other site 504832004606 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832004607 active site 504832004608 phosphorylation site [posttranslational modification] 504832004609 intermolecular recognition site; other site 504832004610 dimerization interface [polypeptide binding]; other site 504832004611 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832004612 metal binding site [ion binding]; metal-binding site 504832004613 active site 504832004614 I-site; other site 504832004615 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 504832004616 hypothetical protein; Provisional; Region: PRK05978 504832004617 ribonuclease R; Region: RNase_R; TIGR02063 504832004618 RNB domain; Region: RNB; pfam00773 504832004619 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 504832004620 RNA binding site [nucleotide binding]; other site 504832004621 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 504832004622 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 504832004623 active site 504832004624 interdomain interaction site; other site 504832004625 putative metal-binding site [ion binding]; other site 504832004626 nucleotide binding site [chemical binding]; other site 504832004627 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 504832004628 domain I; other site 504832004629 DNA binding groove [nucleotide binding] 504832004630 phosphate binding site [ion binding]; other site 504832004631 domain II; other site 504832004632 domain III; other site 504832004633 nucleotide binding site [chemical binding]; other site 504832004634 catalytic site [active] 504832004635 domain IV; other site 504832004636 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 504832004637 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 504832004638 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 504832004639 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 504832004640 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 504832004641 DNA protecting protein DprA; Region: dprA; TIGR00732 504832004642 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 504832004643 dihydroorotase; Validated; Region: PRK09059 504832004644 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 504832004645 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 504832004646 active site 504832004647 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 504832004648 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 504832004649 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 504832004650 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 504832004651 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 504832004652 active site 504832004653 CAAX protease self-immunity; Region: Abi; pfam02517 504832004654 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 504832004655 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 504832004656 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 504832004657 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 504832004658 Chorismate mutase type II; Region: CM_2; smart00830 504832004659 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 504832004660 active site 504832004661 nucleophile elbow; other site 504832004662 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 504832004663 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 504832004664 GatB domain; Region: GatB_Yqey; smart00845 504832004665 LysR family transcriptional regulator; Provisional; Region: PRK14997 504832004666 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832004667 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 504832004668 putative effector binding pocket; other site 504832004669 putative dimerization interface [polypeptide binding]; other site 504832004670 Pirin-related protein [General function prediction only]; Region: COG1741 504832004671 Pirin; Region: Pirin; pfam02678 504832004672 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 504832004673 Isochorismatase family; Region: Isochorismatase; pfam00857 504832004674 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 504832004675 catalytic triad [active] 504832004676 dimer interface [polypeptide binding]; other site 504832004677 conserved cis-peptide bond; other site 504832004678 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 504832004679 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 504832004680 putative ligand binding site [chemical binding]; other site 504832004681 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832004682 dimer interface [polypeptide binding]; other site 504832004683 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 504832004684 putative CheW interface [polypeptide binding]; other site 504832004685 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 504832004686 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 504832004687 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 504832004688 H-NS histone family; Region: Histone_HNS; pfam00816 504832004689 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 504832004690 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 504832004691 Bacterial sugar transferase; Region: Bac_transf; pfam02397 504832004692 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 504832004693 Vi polysaccharide export protein VexA; Provisional; Region: PRK15175 504832004694 Transposase; Region: HTH_Tnp_1; cl17663 504832004695 Integrase core domain; Region: rve; pfam00665 504832004696 Integrase core domain; Region: rve_3; pfam13683 504832004697 Porin subfamily; Region: Porin_2; pfam02530 504832004698 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 504832004699 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832004700 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 504832004701 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832004702 catalytic residue [active] 504832004703 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 504832004704 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 504832004705 dimer interface [polypeptide binding]; other site 504832004706 active site 504832004707 catalytic residue [active] 504832004708 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 504832004709 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 504832004710 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 504832004711 SmpB-tmRNA interface; other site 504832004712 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 504832004713 catalytic triad [active] 504832004714 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 504832004715 Fe-S cluster binding site [ion binding]; other site 504832004716 DNA binding site [nucleotide binding] 504832004717 active site 504832004718 Uncharacterized conserved protein [Function unknown]; Region: COG1432 504832004719 LabA_like proteins; Region: LabA; cd10911 504832004720 putative metal binding site [ion binding]; other site 504832004721 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 504832004722 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 504832004723 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 504832004724 Zn2+ binding site [ion binding]; other site 504832004725 Mg2+ binding site [ion binding]; other site 504832004726 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 504832004727 synthetase active site [active] 504832004728 NTP binding site [chemical binding]; other site 504832004729 metal binding site [ion binding]; metal-binding site 504832004730 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 504832004731 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 504832004732 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 504832004733 active site 504832004734 hydrophilic channel; other site 504832004735 dimerization interface [polypeptide binding]; other site 504832004736 catalytic residues [active] 504832004737 active site lid [active] 504832004738 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 504832004739 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 504832004740 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 504832004741 Catalytic site [active] 504832004742 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 504832004743 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 504832004744 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 504832004745 dimerization interface [polypeptide binding]; other site 504832004746 active site 504832004747 metal binding site [ion binding]; metal-binding site 504832004748 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 504832004749 GTPase Era; Reviewed; Region: era; PRK00089 504832004750 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 504832004751 G1 box; other site 504832004752 GTP/Mg2+ binding site [chemical binding]; other site 504832004753 Switch I region; other site 504832004754 G2 box; other site 504832004755 Switch II region; other site 504832004756 G3 box; other site 504832004757 G4 box; other site 504832004758 G5 box; other site 504832004759 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 504832004760 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 504832004761 Recombination protein O N terminal; Region: RecO_N; pfam11967 504832004762 Recombination protein O C terminal; Region: RecO_C; pfam02565 504832004763 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 504832004764 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 504832004765 CAP-like domain; other site 504832004766 active site 504832004767 primary dimer interface [polypeptide binding]; other site 504832004768 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 504832004769 homodimer interaction site [polypeptide binding]; other site 504832004770 cofactor binding site; other site 504832004771 manganese transport protein MntH; Reviewed; Region: PRK00701 504832004772 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 504832004773 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 504832004774 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 504832004775 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 504832004776 RDD family; Region: RDD; pfam06271 504832004777 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 504832004778 dimer interface [polypeptide binding]; other site 504832004779 allosteric magnesium binding site [ion binding]; other site 504832004780 active site 504832004781 aspartate-rich active site metal binding site; other site 504832004782 Schiff base residues; other site 504832004783 Transcriptional regulators [Transcription]; Region: MarR; COG1846 504832004784 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 504832004785 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 504832004786 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 504832004787 dimer interface [polypeptide binding]; other site 504832004788 active site 504832004789 glycine-pyridoxal phosphate binding site [chemical binding]; other site 504832004790 folate binding site [chemical binding]; other site 504832004791 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 504832004792 ATP cone domain; Region: ATP-cone; pfam03477 504832004793 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 504832004794 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 504832004795 catalytic motif [active] 504832004796 Zn binding site [ion binding]; other site 504832004797 RibD C-terminal domain; Region: RibD_C; cl17279 504832004798 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 504832004799 Lumazine binding domain; Region: Lum_binding; pfam00677 504832004800 Lumazine binding domain; Region: Lum_binding; pfam00677 504832004801 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 504832004802 homopentamer interface [polypeptide binding]; other site 504832004803 active site 504832004804 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 504832004805 putative RNA binding site [nucleotide binding]; other site 504832004806 thiamine monophosphate kinase; Provisional; Region: PRK05731 504832004807 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 504832004808 ATP binding site [chemical binding]; other site 504832004809 dimerization interface [polypeptide binding]; other site 504832004810 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 504832004811 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 504832004812 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 504832004813 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 504832004814 putative substrate translocation pore; other site 504832004815 Amino acid synthesis; Region: AA_synth; pfam06684 504832004816 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832004817 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 504832004818 non-specific DNA binding site [nucleotide binding]; other site 504832004819 salt bridge; other site 504832004820 sequence-specific DNA binding site [nucleotide binding]; other site 504832004821 Cupin domain; Region: Cupin_2; pfam07883 504832004822 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 504832004823 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 504832004824 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 504832004825 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 504832004826 putative phosphate acyltransferase; Provisional; Region: PRK05331 504832004827 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 504832004828 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 504832004829 dimer interface [polypeptide binding]; other site 504832004830 active site 504832004831 CoA binding pocket [chemical binding]; other site 504832004832 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 504832004833 IHF dimer interface [polypeptide binding]; other site 504832004834 IHF - DNA interface [nucleotide binding]; other site 504832004835 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 504832004836 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 504832004837 DNA binding residues [nucleotide binding] 504832004838 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 504832004839 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 504832004840 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 504832004841 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 504832004842 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 504832004843 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 504832004844 putative active site [active] 504832004845 Predicted permeases [General function prediction only]; Region: COG0795 504832004846 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 504832004847 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 504832004848 Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane]; Region: WcaJ; COG2148 504832004849 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 504832004850 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832004851 Chain length determinant protein; Region: Wzz; pfam02706 504832004852 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 504832004853 AAA domain; Region: AAA_31; pfam13614 504832004854 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 504832004855 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 504832004856 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 504832004857 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 504832004858 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 504832004859 Iron permease FTR1 family; Region: FTR1; cl00475 504832004860 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK05994 504832004861 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 504832004862 homodimer interface [polypeptide binding]; other site 504832004863 substrate-cofactor binding pocket; other site 504832004864 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832004865 catalytic residue [active] 504832004866 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 504832004867 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 504832004868 CoenzymeA binding site [chemical binding]; other site 504832004869 subunit interaction site [polypeptide binding]; other site 504832004870 PHB binding site; other site 504832004871 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 504832004872 23S rRNA interface [nucleotide binding]; other site 504832004873 L3 interface [polypeptide binding]; other site 504832004874 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 504832004875 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832004876 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832004877 metal binding site [ion binding]; metal-binding site 504832004878 active site 504832004879 I-site; other site 504832004880 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 504832004881 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 504832004882 Domain of unknown function DUF20; Region: UPF0118; pfam01594 504832004883 glutamine synthetase; Provisional; Region: glnA; PRK09469 504832004884 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 504832004885 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 504832004886 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 504832004887 Nitrogen regulatory protein P-II; Region: P-II; smart00938 504832004888 Uncharacterized conserved protein [Function unknown]; Region: COG0062 504832004889 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 504832004890 putative substrate binding site [chemical binding]; other site 504832004891 putative ATP binding site [chemical binding]; other site 504832004892 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 504832004893 Multicopper oxidase; Region: Cu-oxidase; pfam00394 504832004894 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 504832004895 trigger factor; Provisional; Region: tig; PRK01490 504832004896 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 504832004897 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 504832004898 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 504832004899 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 504832004900 oligomer interface [polypeptide binding]; other site 504832004901 active site residues [active] 504832004902 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 504832004903 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 504832004904 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 504832004905 Walker A motif; other site 504832004906 ATP binding site [chemical binding]; other site 504832004907 Walker B motif; other site 504832004908 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 504832004909 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 504832004910 Found in ATP-dependent protease La (LON); Region: LON; smart00464 504832004911 Found in ATP-dependent protease La (LON); Region: LON; smart00464 504832004912 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 504832004913 Walker A motif; other site 504832004914 ATP binding site [chemical binding]; other site 504832004915 Walker B motif; other site 504832004916 arginine finger; other site 504832004917 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 504832004918 Methyltransferase domain; Region: Methyltransf_25; pfam13649 504832004919 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832004920 peptidase T; Region: peptidase-T; TIGR01882 504832004921 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 504832004922 metal binding site [ion binding]; metal-binding site 504832004923 dimer interface [polypeptide binding]; other site 504832004924 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 504832004925 IHF - DNA interface [nucleotide binding]; other site 504832004926 IHF dimer interface [polypeptide binding]; other site 504832004927 tartrate dehydrogenase; Region: TTC; TIGR02089 504832004928 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 504832004929 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 504832004930 NADH dehydrogenase subunit B; Validated; Region: PRK06411 504832004931 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 504832004932 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 504832004933 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 504832004934 active site 2 [active] 504832004935 active site 1 [active] 504832004936 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 504832004937 NADH dehydrogenase subunit D; Validated; Region: PRK06075 504832004938 NADH dehydrogenase subunit E; Validated; Region: PRK07539 504832004939 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 504832004940 putative dimer interface [polypeptide binding]; other site 504832004941 [2Fe-2S] cluster binding site [ion binding]; other site 504832004942 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 504832004943 SLBB domain; Region: SLBB; pfam10531 504832004944 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 504832004945 NADH dehydrogenase subunit G; Validated; Region: PRK09130 504832004946 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 504832004947 catalytic loop [active] 504832004948 iron binding site [ion binding]; other site 504832004949 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 504832004950 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 504832004951 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 504832004952 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 504832004953 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 504832004954 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 504832004955 4Fe-4S binding domain; Region: Fer4; cl02805 504832004956 4Fe-4S binding domain; Region: Fer4; pfam00037 504832004957 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 504832004958 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 504832004959 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 504832004960 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 504832004961 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 504832004962 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 504832004963 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 504832004964 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 504832004965 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 504832004966 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 504832004967 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 504832004968 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 504832004969 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 504832004970 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 504832004971 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 504832004972 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 504832004973 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 504832004974 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832004975 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 504832004976 dimer interface [polypeptide binding]; other site 504832004977 substrate binding site [chemical binding]; other site 504832004978 metal binding site [ion binding]; metal-binding site 504832004979 Protein of unknown function (DUF1467); Region: DUF1467; pfam07330 504832004980 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 504832004981 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 504832004982 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 504832004983 N-terminal plug; other site 504832004984 ligand-binding site [chemical binding]; other site 504832004985 BNR repeat-like domain; Region: BNR_2; pfam13088 504832004986 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 504832004987 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832004988 catalytic residues [active] 504832004989 Protein of unknown function (DUF461); Region: DUF461; pfam04314 504832004990 prolyl-tRNA synthetase; Provisional; Region: PRK12325 504832004991 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 504832004992 dimer interface [polypeptide binding]; other site 504832004993 motif 1; other site 504832004994 active site 504832004995 motif 2; other site 504832004996 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 504832004997 active site 504832004998 motif 3; other site 504832004999 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 504832005000 anticodon binding site; other site 504832005001 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 504832005002 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 504832005003 FtsX-like permease family; Region: FtsX; pfam02687 504832005004 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 504832005005 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 504832005006 Walker A/P-loop; other site 504832005007 ATP binding site [chemical binding]; other site 504832005008 Q-loop/lid; other site 504832005009 ABC transporter signature motif; other site 504832005010 Walker B; other site 504832005011 D-loop; other site 504832005012 H-loop/switch region; other site 504832005013 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 504832005014 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 504832005015 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 504832005016 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 504832005017 putative active site [active] 504832005018 putative PHP Thumb interface [polypeptide binding]; other site 504832005019 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 504832005020 generic binding surface II; other site 504832005021 generic binding surface I; other site 504832005022 Uncharacterized protein containing caspase domain [General function prediction only]; Region: COG4249 504832005023 Caspase domain; Region: Peptidase_C14; pfam00656 504832005024 30S ribosomal protein S2/unknown domain fusion protein; Provisional; Region: rpsB; PRK12311 504832005025 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 504832005026 rRNA interaction site [nucleotide binding]; other site 504832005027 S8 interaction site; other site 504832005028 putative laminin-1 binding site; other site 504832005029 Uncharacterized conserved protein [Function unknown]; Region: COG3743 504832005030 elongation factor Ts; Provisional; Region: tsf; PRK09377 504832005031 UBA/TS-N domain; Region: UBA; pfam00627 504832005032 Elongation factor TS; Region: EF_TS; pfam00889 504832005033 Elongation factor TS; Region: EF_TS; pfam00889 504832005034 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 504832005035 putative nucleotide binding site [chemical binding]; other site 504832005036 uridine monophosphate binding site [chemical binding]; other site 504832005037 homohexameric interface [polypeptide binding]; other site 504832005038 ribosome recycling factor; Reviewed; Region: frr; PRK00083 504832005039 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 504832005040 hinge region; other site 504832005041 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14834 504832005042 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 504832005043 catalytic residue [active] 504832005044 putative FPP diphosphate binding site; other site 504832005045 putative FPP binding hydrophobic cleft; other site 504832005046 dimer interface [polypeptide binding]; other site 504832005047 putative IPP diphosphate binding site; other site 504832005048 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 504832005049 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 504832005050 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 504832005051 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 504832005052 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 504832005053 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 504832005054 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 504832005055 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 504832005056 active site 504832005057 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 504832005058 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 504832005059 putative substrate binding region [chemical binding]; other site 504832005060 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 504832005061 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 504832005062 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 504832005063 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 504832005064 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 504832005065 Surface antigen; Region: Bac_surface_Ag; pfam01103 504832005066 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 504832005067 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 504832005068 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 504832005069 active site 504832005070 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 504832005071 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 504832005072 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 504832005073 PAS domain; Region: PAS_9; pfam13426 504832005074 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 504832005075 putative active site [active] 504832005076 heme pocket [chemical binding]; other site 504832005077 HAMP domain; Region: HAMP; pfam00672 504832005078 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832005079 dimer interface [polypeptide binding]; other site 504832005080 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 504832005081 putative CheW interface [polypeptide binding]; other site 504832005082 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 504832005083 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 504832005084 dimer interface [polypeptide binding]; other site 504832005085 active site 504832005086 citrylCoA binding site [chemical binding]; other site 504832005087 NADH binding [chemical binding]; other site 504832005088 cationic pore residues; other site 504832005089 oxalacetate/citrate binding site [chemical binding]; other site 504832005090 coenzyme A binding site [chemical binding]; other site 504832005091 catalytic triad [active] 504832005092 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 504832005093 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 504832005094 HIGH motif; other site 504832005095 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 504832005096 active site 504832005097 KMSKS motif; other site 504832005098 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 504832005099 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 504832005100 active site 504832005101 HIGH motif; other site 504832005102 nucleotide binding site [chemical binding]; other site 504832005103 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 504832005104 KMSKS motif; other site 504832005105 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 504832005106 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 504832005107 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 504832005108 Competence protein; Region: Competence; pfam03772 504832005109 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 504832005110 Response regulator receiver domain; Region: Response_reg; pfam00072 504832005111 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832005112 active site 504832005113 phosphorylation site [posttranslational modification] 504832005114 intermolecular recognition site; other site 504832005115 dimerization interface [polypeptide binding]; other site 504832005116 Histidine kinase; Region: HisKA_2; pfam07568 504832005117 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 504832005118 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 504832005119 ATP binding site [chemical binding]; other site 504832005120 Mg2+ binding site [ion binding]; other site 504832005121 G-X-G motif; other site 504832005122 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 504832005123 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832005124 active site 504832005125 phosphorylation site [posttranslational modification] 504832005126 intermolecular recognition site; other site 504832005127 dimerization interface [polypeptide binding]; other site 504832005128 CHASE3 domain; Region: CHASE3; pfam05227 504832005129 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 504832005130 dimer interface [polypeptide binding]; other site 504832005131 phosphorylation site [posttranslational modification] 504832005132 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 504832005133 ATP binding site [chemical binding]; other site 504832005134 Mg2+ binding site [ion binding]; other site 504832005135 G-X-G motif; other site 504832005136 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 504832005137 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 504832005138 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 504832005139 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 504832005140 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 504832005141 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 504832005142 carboxyltransferase (CT) interaction site; other site 504832005143 biotinylation site [posttranslational modification]; other site 504832005144 Dehydroquinase class II; Region: DHquinase_II; pfam01220 504832005145 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 504832005146 trimer interface [polypeptide binding]; other site 504832005147 active site 504832005148 dimer interface [polypeptide binding]; other site 504832005149 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 504832005150 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 504832005151 catalytic residues [active] 504832005152 Peptidase family M48; Region: Peptidase_M48; cl12018 504832005153 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 504832005154 TPR motif; other site 504832005155 TPR repeat; Region: TPR_11; pfam13414 504832005156 binding surface 504832005157 aspartate aminotransferase; Provisional; Region: PRK05764 504832005158 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 504832005159 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832005160 homodimer interface [polypeptide binding]; other site 504832005161 catalytic residue [active] 504832005162 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 504832005163 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 504832005164 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 504832005165 AMIN domain; Region: AMIN; pfam11741 504832005166 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 504832005167 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 504832005168 active site 504832005169 metal binding site [ion binding]; metal-binding site 504832005170 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 504832005171 Transglycosylase; Region: Transgly; pfam00912 504832005172 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 504832005173 peptide chain release factor 2; Provisional; Region: PRK07342 504832005174 This domain is found in peptide chain release factors; Region: PCRF; smart00937 504832005175 RF-1 domain; Region: RF-1; pfam00472 504832005176 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 504832005177 nucleoside/Zn binding site; other site 504832005178 dimer interface [polypeptide binding]; other site 504832005179 catalytic motif [active] 504832005180 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 504832005181 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 504832005182 Peptidase family M23; Region: Peptidase_M23; pfam01551 504832005183 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 504832005184 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832005185 catalytic triad [active] 504832005186 Protein of unknown function; Region: DUF3971; pfam13116 504832005187 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 504832005188 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 504832005189 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 504832005190 active site 504832005191 HIGH motif; other site 504832005192 dimer interface [polypeptide binding]; other site 504832005193 KMSKS motif; other site 504832005194 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 504832005195 RNA binding surface [nucleotide binding]; other site 504832005196 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 504832005197 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 504832005198 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 504832005199 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 504832005200 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832005201 catalytic residue [active] 504832005202 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 504832005203 putative ABC transporter; Region: ycf24; CHL00085 504832005204 FeS assembly ATPase SufC; Region: sufC; TIGR01978 504832005205 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 504832005206 Walker A/P-loop; other site 504832005207 ATP binding site [chemical binding]; other site 504832005208 Q-loop/lid; other site 504832005209 ABC transporter signature motif; other site 504832005210 Walker B; other site 504832005211 D-loop; other site 504832005212 H-loop/switch region; other site 504832005213 FeS assembly protein SufD; Region: sufD; TIGR01981 504832005214 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 504832005215 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 504832005216 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 504832005217 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832005218 catalytic residue [active] 504832005219 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 504832005220 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 504832005221 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832005222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832005223 metal binding site [ion binding]; metal-binding site 504832005224 active site 504832005225 I-site; other site 504832005226 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 504832005227 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 504832005228 ATP binding site [chemical binding]; other site 504832005229 Mg++ binding site [ion binding]; other site 504832005230 motif III; other site 504832005231 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 504832005232 nucleotide binding region [chemical binding]; other site 504832005233 ATP-binding site [chemical binding]; other site 504832005234 hypothetical protein; Provisional; Region: PRK06185 504832005235 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832005236 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 504832005237 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 504832005238 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 504832005239 Mg2+ binding site [ion binding]; other site 504832005240 G-X-G motif; other site 504832005241 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 504832005242 anchoring element; other site 504832005243 dimer interface [polypeptide binding]; other site 504832005244 ATP binding site [chemical binding]; other site 504832005245 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 504832005246 active site 504832005247 putative metal-binding site [ion binding]; other site 504832005248 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 504832005249 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 504832005250 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 504832005251 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 504832005252 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 504832005253 MAPEG family; Region: MAPEG; pfam01124 504832005254 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 504832005255 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 504832005256 U5 snRNP spliceosome subunit [RNA processing and modification]; Region: PRP8; COG5178 504832005257 aminotransferase; Validated; Region: PRK09148 504832005258 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 504832005259 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832005260 homodimer interface [polypeptide binding]; other site 504832005261 catalytic residue [active] 504832005262 homoserine dehydrogenase; Provisional; Region: PRK06349 504832005263 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 504832005264 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 504832005265 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 504832005266 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 504832005267 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 504832005268 putative active site [active] 504832005269 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 504832005270 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 504832005271 motif II; other site 504832005272 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 504832005273 DHH family; Region: DHH; pfam01368 504832005274 DHHA1 domain; Region: DHHA1; pfam02272 504832005275 lytic murein transglycosylase; Region: MltB_2; TIGR02283 504832005276 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 504832005277 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832005278 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832005279 spermidine synthase; Provisional; Region: PRK00811 504832005280 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 504832005281 S-adenosylmethionine binding site [chemical binding]; other site 504832005282 S-adenosylmethionine decarboxylase proenzyme, Bacillus form; Region: SAM_DCase_Bsu; TIGR03330 504832005283 elongation factor P; Validated; Region: PRK00529 504832005284 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 504832005285 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 504832005286 RNA binding site [nucleotide binding]; other site 504832005287 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 504832005288 RNA binding site [nucleotide binding]; other site 504832005289 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 504832005290 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 504832005291 motif 1; other site 504832005292 dimer interface [polypeptide binding]; other site 504832005293 active site 504832005294 motif 2; other site 504832005295 motif 3; other site 504832005296 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 504832005297 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 504832005298 FeS/SAM binding site; other site 504832005299 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 504832005300 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 504832005301 Flavoprotein; Region: Flavoprotein; pfam02441 504832005302 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 504832005303 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 504832005304 dimer interface [polypeptide binding]; other site 504832005305 active site 504832005306 metal binding site [ion binding]; metal-binding site 504832005307 glutathione binding site [chemical binding]; other site 504832005308 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 504832005309 DNA-binding site [nucleotide binding]; DNA binding site 504832005310 RNA-binding motif; other site 504832005311 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 504832005312 DNA-binding site [nucleotide binding]; DNA binding site 504832005313 RNA-binding motif; other site 504832005314 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 504832005315 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832005316 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 504832005317 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005318 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005319 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005320 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005321 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005322 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005323 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005324 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005325 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005326 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005327 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005328 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 504832005329 VCBS repeat; Region: VCBS_repeat; TIGR01965 504832005330 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 504832005331 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 504832005332 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 504832005333 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832005334 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 504832005335 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 504832005336 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832005337 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 504832005338 Walker A/P-loop; other site 504832005339 ATP binding site [chemical binding]; other site 504832005340 Q-loop/lid; other site 504832005341 ABC transporter signature motif; other site 504832005342 Walker B; other site 504832005343 D-loop; other site 504832005344 H-loop/switch region; other site 504832005345 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 504832005346 OpgC protein; Region: OpgC_C; pfam10129 504832005347 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 504832005348 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 504832005349 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 504832005350 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 504832005351 active site 504832005352 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 504832005353 Putative Catalytic site; other site 504832005354 DXD motif; other site 504832005355 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 504832005356 cystathionine beta-lyase; Provisional; Region: PRK05967 504832005357 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 504832005358 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832005359 catalytic residue [active] 504832005360 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 504832005361 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 504832005362 substrate binding pocket [chemical binding]; other site 504832005363 membrane-bound complex binding site; other site 504832005364 hinge residues; other site 504832005365 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 504832005366 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 504832005367 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 504832005368 putative PBP binding loops; other site 504832005369 dimer interface [polypeptide binding]; other site 504832005370 ABC-ATPase subunit interface; other site 504832005371 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 504832005372 dimer interface [polypeptide binding]; other site 504832005373 conserved gate region; other site 504832005374 putative PBP binding loops; other site 504832005375 ABC-ATPase subunit interface; other site 504832005376 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 504832005377 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 504832005378 Walker A/P-loop; other site 504832005379 ATP binding site [chemical binding]; other site 504832005380 Q-loop/lid; other site 504832005381 ABC transporter signature motif; other site 504832005382 Walker B; other site 504832005383 D-loop; other site 504832005384 H-loop/switch region; other site 504832005385 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 504832005386 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 504832005387 dimer interface [polypeptide binding]; other site 504832005388 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832005389 catalytic residue [active] 504832005390 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 504832005391 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 504832005392 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832005393 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832005394 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 504832005395 Protein export membrane protein; Region: SecD_SecF; cl14618 504832005396 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 504832005397 Protein export membrane protein; Region: SecD_SecF; cl14618 504832005398 DTW domain; Region: DTW; cl01221 504832005399 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 504832005400 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 504832005401 substrate binding site [chemical binding]; other site 504832005402 oxyanion hole (OAH) forming residues; other site 504832005403 trimer interface [polypeptide binding]; other site 504832005404 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832005405 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832005406 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 504832005407 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 504832005408 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 504832005409 active site 504832005410 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832005411 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832005412 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832005413 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832005414 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 504832005415 Dehydratase family; Region: ILVD_EDD; pfam00920 504832005416 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 504832005417 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_12; cd08491 504832005418 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 504832005419 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 504832005420 dimer interface [polypeptide binding]; other site 504832005421 conserved gate region; other site 504832005422 putative PBP binding loops; other site 504832005423 ABC-ATPase subunit interface; other site 504832005424 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 504832005425 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 504832005426 dimer interface [polypeptide binding]; other site 504832005427 conserved gate region; other site 504832005428 putative PBP binding loops; other site 504832005429 ABC-ATPase subunit interface; other site 504832005430 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 504832005431 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832005432 Walker A/P-loop; other site 504832005433 ATP binding site [chemical binding]; other site 504832005434 Q-loop/lid; other site 504832005435 ABC transporter signature motif; other site 504832005436 Walker B; other site 504832005437 D-loop; other site 504832005438 H-loop/switch region; other site 504832005439 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832005440 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832005441 Walker A/P-loop; other site 504832005442 ATP binding site [chemical binding]; other site 504832005443 Q-loop/lid; other site 504832005444 ABC transporter signature motif; other site 504832005445 Walker B; other site 504832005446 D-loop; other site 504832005447 H-loop/switch region; other site 504832005448 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 504832005449 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 504832005450 heme-binding site [chemical binding]; other site 504832005451 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832005452 dimer interface [polypeptide binding]; other site 504832005453 putative CheW interface [polypeptide binding]; other site 504832005454 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 504832005455 S-adenosylmethionine binding site [chemical binding]; other site 504832005456 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 504832005457 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 504832005458 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 504832005459 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 504832005460 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 504832005461 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 504832005462 HIGH motif; other site 504832005463 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 504832005464 active site 504832005465 KMSKS motif; other site 504832005466 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 504832005467 tRNA binding surface [nucleotide binding]; other site 504832005468 anticodon binding site; other site 504832005469 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 504832005470 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 504832005471 active site 504832005472 DNA binding site [nucleotide binding] 504832005473 lipoyl synthase; Provisional; Region: PRK05481 504832005474 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 504832005475 FeS/SAM binding site; other site 504832005476 Competence-damaged protein; Region: CinA; pfam02464 504832005477 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 504832005478 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 504832005479 substrate binding site; other site 504832005480 dimer interface; other site 504832005481 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 504832005482 homotrimer interaction site [polypeptide binding]; other site 504832005483 zinc binding site [ion binding]; other site 504832005484 CDP-binding sites; other site 504832005485 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 504832005486 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 504832005487 FMN binding site [chemical binding]; other site 504832005488 active site 504832005489 catalytic residues [active] 504832005490 substrate binding site [chemical binding]; other site 504832005491 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 504832005492 PAS domain; Region: PAS; smart00091 504832005493 putative active site [active] 504832005494 heme pocket [chemical binding]; other site 504832005495 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 504832005496 dimer interface [polypeptide binding]; other site 504832005497 phosphorylation site [posttranslational modification] 504832005498 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 504832005499 ATP binding site [chemical binding]; other site 504832005500 Mg2+ binding site [ion binding]; other site 504832005501 G-X-G motif; other site 504832005502 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 504832005503 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832005504 active site 504832005505 phosphorylation site [posttranslational modification] 504832005506 intermolecular recognition site; other site 504832005507 dimerization interface [polypeptide binding]; other site 504832005508 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 504832005509 Walker A motif; other site 504832005510 ATP binding site [chemical binding]; other site 504832005511 Walker B motif; other site 504832005512 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 504832005513 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 504832005514 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 504832005515 dimerization interface [polypeptide binding]; other site 504832005516 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 504832005517 dimer interface [polypeptide binding]; other site 504832005518 phosphorylation site [posttranslational modification] 504832005519 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 504832005520 ATP binding site [chemical binding]; other site 504832005521 Mg2+ binding site [ion binding]; other site 504832005522 G-X-G motif; other site 504832005523 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 504832005524 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832005525 active site 504832005526 phosphorylation site [posttranslational modification] 504832005527 intermolecular recognition site; other site 504832005528 dimerization interface [polypeptide binding]; other site 504832005529 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 504832005530 Walker A motif; other site 504832005531 ATP binding site [chemical binding]; other site 504832005532 Walker B motif; other site 504832005533 arginine finger; other site 504832005534 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 504832005535 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 504832005536 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 504832005537 homodimer interface [polypeptide binding]; other site 504832005538 substrate-cofactor binding pocket; other site 504832005539 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832005540 catalytic residue [active] 504832005541 bacterial Hfq-like; Region: Hfq; cd01716 504832005542 hexamer interface [polypeptide binding]; other site 504832005543 Sm1 motif; other site 504832005544 RNA binding site [nucleotide binding]; other site 504832005545 Sm2 motif; other site 504832005546 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 504832005547 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 504832005548 HflX GTPase family; Region: HflX; cd01878 504832005549 G1 box; other site 504832005550 GTP/Mg2+ binding site [chemical binding]; other site 504832005551 Switch I region; other site 504832005552 G2 box; other site 504832005553 G3 box; other site 504832005554 Switch II region; other site 504832005555 G4 box; other site 504832005556 G5 box; other site 504832005557 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 504832005558 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 504832005559 homodimer interface [polypeptide binding]; other site 504832005560 metal binding site [ion binding]; metal-binding site 504832005561 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 504832005562 homodimer interface [polypeptide binding]; other site 504832005563 active site 504832005564 putative chemical substrate binding site [chemical binding]; other site 504832005565 metal binding site [ion binding]; metal-binding site 504832005566 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 504832005567 Ligand Binding Site [chemical binding]; other site 504832005568 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 504832005569 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832005570 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 504832005571 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832005572 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 504832005573 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 504832005574 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 504832005575 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; cl01495 504832005576 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 504832005577 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 504832005578 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832005579 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 504832005580 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 504832005581 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 504832005582 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 504832005583 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 504832005584 SLBB domain; Region: SLBB; pfam10531 504832005585 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832005586 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 504832005587 active site 504832005588 metal binding site [ion binding]; metal-binding site 504832005589 Bacterial sugar transferase; Region: Bac_transf; pfam02397 504832005590 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 504832005591 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 504832005592 Substrate binding site; other site 504832005593 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 504832005594 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 504832005595 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 504832005596 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 504832005597 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 504832005598 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 504832005599 putative hydrolase; Provisional; Region: PRK02113 504832005600 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 504832005601 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 504832005602 active site 504832005603 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 504832005604 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 504832005605 active site 504832005606 HIGH motif; other site 504832005607 KMSKS motif; other site 504832005608 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 504832005609 tRNA binding surface [nucleotide binding]; other site 504832005610 anticodon binding site; other site 504832005611 DNA polymerase III subunit delta'; Validated; Region: PRK07471 504832005612 DNA polymerase III subunit delta'; Validated; Region: PRK08485 504832005613 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 504832005614 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 504832005615 TMP-binding site; other site 504832005616 ATP-binding site [chemical binding]; other site 504832005617 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 504832005618 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 504832005619 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 504832005620 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 504832005621 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 504832005622 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 504832005623 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 504832005624 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 504832005625 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 504832005626 Phage capsid family; Region: Phage_capsid; pfam05065 504832005627 AAA domain; Region: AAA_25; pfam13481 504832005628 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 504832005629 Walker A motif; other site 504832005630 ATP binding site [chemical binding]; other site 504832005631 Walker B motif; other site 504832005632 Toprim domain; Region: Toprim_3; pfam13362 504832005633 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 504832005634 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 504832005635 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 504832005636 active site 504832005637 Int/Topo IB signature motif; other site 504832005638 Phage Terminase; Region: Terminase_1; pfam03354 504832005639 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 504832005640 Phage terminase, small subunit; Region: Terminase_4; pfam05119 504832005641 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 504832005642 oligomerization interface [polypeptide binding]; other site 504832005643 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 504832005644 Phage capsid family; Region: Phage_capsid; pfam05065 504832005645 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 504832005646 Phage-related protein [Function unknown]; Region: COG4695; cl01923 504832005647 Phage portal protein; Region: Phage_portal; pfam04860 504832005648 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 504832005649 Walker A motif; other site 504832005650 ATP binding site [chemical binding]; other site 504832005651 Walker B motif; other site 504832005652 integrase; Provisional; Region: PRK09692 504832005653 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 504832005654 active site 504832005655 Int/Topo IB signature motif; other site 504832005656 AAA domain; Region: AAA_13; pfam13166 504832005657 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 504832005658 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 504832005659 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 504832005660 DNA binding residues [nucleotide binding] 504832005661 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 504832005662 dimer interface [polypeptide binding]; other site 504832005663 putative metal binding site [ion binding]; other site 504832005664 nitrobindin heme-binding domain; Region: nitrobindin; cd07828 504832005665 heme-binding site [chemical binding]; other site 504832005666 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 504832005667 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832005668 Multicopper oxidase; Region: Cu-oxidase; pfam00394 504832005669 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 504832005670 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 504832005671 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832005672 Walker A/P-loop; other site 504832005673 ATP binding site [chemical binding]; other site 504832005674 Q-loop/lid; other site 504832005675 ABC transporter signature motif; other site 504832005676 Walker B; other site 504832005677 D-loop; other site 504832005678 H-loop/switch region; other site 504832005679 TOBE domain; Region: TOBE_2; pfam08402 504832005680 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 504832005681 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 504832005682 dimer interface [polypeptide binding]; other site 504832005683 conserved gate region; other site 504832005684 putative PBP binding loops; other site 504832005685 ABC-ATPase subunit interface; other site 504832005686 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 504832005687 dimer interface [polypeptide binding]; other site 504832005688 conserved gate region; other site 504832005689 putative PBP binding loops; other site 504832005690 ABC-ATPase subunit interface; other site 504832005691 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 504832005692 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 504832005693 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 504832005694 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 504832005695 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832005696 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 504832005697 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 504832005698 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 504832005699 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 504832005700 ligand binding site [chemical binding]; other site 504832005701 flexible hinge region; other site 504832005702 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 504832005703 hypothetical protein; Validated; Region: PRK08245 504832005704 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 504832005705 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 504832005706 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 504832005707 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 504832005708 putative active site [active] 504832005709 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 504832005710 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 504832005711 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 504832005712 FeS/SAM binding site; other site 504832005713 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 504832005714 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 504832005715 NADP binding site [chemical binding]; other site 504832005716 dimer interface [polypeptide binding]; other site 504832005717 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 504832005718 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 504832005719 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 504832005720 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 504832005721 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; pfam08755 504832005722 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 504832005723 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 504832005724 N-terminal plug; other site 504832005725 ligand-binding site [chemical binding]; other site 504832005726 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 504832005727 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 504832005728 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 504832005729 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 504832005730 AMP-binding enzyme; Region: AMP-binding; pfam00501 504832005731 acyl-activating enzyme (AAE) consensus motif; other site 504832005732 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 504832005733 active site 504832005734 CoA binding site [chemical binding]; other site 504832005735 AMP binding site [chemical binding]; other site 504832005736 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832005737 PRC-barrel domain; Region: PRC; pfam05239 504832005738 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 504832005739 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 504832005740 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 504832005741 ATP binding site [chemical binding]; other site 504832005742 putative Mg++ binding site [ion binding]; other site 504832005743 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 504832005744 nucleotide binding region [chemical binding]; other site 504832005745 ATP-binding site [chemical binding]; other site 504832005746 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 504832005747 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 504832005748 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 504832005749 generic binding surface II; other site 504832005750 ssDNA binding site; other site 504832005751 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 504832005752 ATP binding site [chemical binding]; other site 504832005753 putative Mg++ binding site [ion binding]; other site 504832005754 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 504832005755 nucleotide binding region [chemical binding]; other site 504832005756 ATP-binding site [chemical binding]; other site 504832005757 Uncharacterized conserved protein [Function unknown]; Region: COG2928 504832005758 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 504832005759 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 504832005760 glutaminase active site [active] 504832005761 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 504832005762 dimer interface [polypeptide binding]; other site 504832005763 active site 504832005764 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 504832005765 dimer interface [polypeptide binding]; other site 504832005766 active site 504832005767 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 504832005768 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 504832005769 Substrate binding site; other site 504832005770 Mg++ binding site; other site 504832005771 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 504832005772 active site 504832005773 substrate binding site [chemical binding]; other site 504832005774 CoA binding site [chemical binding]; other site 504832005775 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 504832005776 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 504832005777 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 504832005778 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 504832005779 active site 504832005780 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 504832005781 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832005782 dimer interface [polypeptide binding]; other site 504832005783 putative CheW interface [polypeptide binding]; other site 504832005784 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 504832005785 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 504832005786 dimer interface [polypeptide binding]; other site 504832005787 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832005788 catalytic residue [active] 504832005789 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 504832005790 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 504832005791 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 504832005792 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 504832005793 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 504832005794 active site 504832005795 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 504832005796 active site 504832005797 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 504832005798 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 504832005799 active site 504832005800 (T/H)XGH motif; other site 504832005801 DNA gyrase subunit A; Validated; Region: PRK05560 504832005802 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 504832005803 CAP-like domain; other site 504832005804 active site 504832005805 primary dimer interface [polypeptide binding]; other site 504832005806 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 504832005807 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 504832005808 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 504832005809 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 504832005810 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 504832005811 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 504832005812 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 504832005813 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 504832005814 dimer interface [polypeptide binding]; other site 504832005815 ssDNA binding site [nucleotide binding]; other site 504832005816 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832005817 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 504832005818 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 504832005819 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 504832005820 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 504832005821 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 504832005822 Predicted acetyltransferase [General function prediction only]; Region: COG2388 504832005823 Predicted acetyltransferase [General function prediction only]; Region: COG2388 504832005824 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 504832005825 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 504832005826 Isochorismatase family; Region: Isochorismatase; pfam00857 504832005827 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 504832005828 catalytic triad [active] 504832005829 dimer interface [polypeptide binding]; other site 504832005830 conserved cis-peptide bond; other site 504832005831 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832005832 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2368 504832005833 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 504832005834 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 504832005835 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 504832005836 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 504832005837 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 504832005838 intracellular protease, PfpI family; Region: PfpI; TIGR01382 504832005839 proposed catalytic triad [active] 504832005840 conserved cys residue [active] 504832005841 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 504832005842 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 504832005843 Glucose inhibited division protein A; Region: GIDA; pfam01134 504832005844 Squalene/phytoene synthase; Region: SQS_PSY; pfam00494 504832005845 substrate binding pocket [chemical binding]; other site 504832005846 substrate-Mg2+ binding site; other site 504832005847 aspartate-rich region 1; other site 504832005848 aspartate-rich region 2; other site 504832005849 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 504832005850 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 504832005851 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 504832005852 Protein export membrane protein; Region: SecD_SecF; pfam02355 504832005853 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 504832005854 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 504832005855 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 504832005856 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 504832005857 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 504832005858 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 504832005859 Walker A motif; other site 504832005860 ATP binding site [chemical binding]; other site 504832005861 Walker B motif; other site 504832005862 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 504832005863 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 504832005864 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 504832005865 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 504832005866 Peptidase family M23; Region: Peptidase_M23; pfam01551 504832005867 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 504832005868 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 504832005869 S-adenosylmethionine binding site [chemical binding]; other site 504832005870 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 504832005871 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832005872 active site 504832005873 phosphorylation site [posttranslational modification] 504832005874 intermolecular recognition site; other site 504832005875 dimerization interface [polypeptide binding]; other site 504832005876 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 504832005877 seryl-tRNA synthetase; Provisional; Region: PRK05431 504832005878 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 504832005879 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 504832005880 dimer interface [polypeptide binding]; other site 504832005881 active site 504832005882 motif 1; other site 504832005883 motif 2; other site 504832005884 motif 3; other site 504832005885 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 504832005886 twin arginine-targeting protein translocase TatB; Region: tatB; TIGR01410 504832005887 twin arginine translocase protein A; Provisional; Region: tatA; PRK00720 504832005888 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 504832005889 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 504832005890 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 504832005891 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 504832005892 catalytic residues [active] 504832005893 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 504832005894 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 504832005895 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 504832005896 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 504832005897 Sporulation related domain; Region: SPOR; pfam05036 504832005898 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 504832005899 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 504832005900 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 504832005901 active site 504832005902 HIGH motif; other site 504832005903 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 504832005904 KMSK motif region; other site 504832005905 tRNA binding surface [nucleotide binding]; other site 504832005906 DALR anticodon binding domain; Region: DALR_1; smart00836 504832005907 anticodon binding site; other site 504832005908 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 504832005909 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 504832005910 Zn2+ binding site [ion binding]; other site 504832005911 Mg2+ binding site [ion binding]; other site 504832005912 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 504832005913 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 504832005914 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 504832005915 putative catalytic site [active] 504832005916 putative phosphate binding site [ion binding]; other site 504832005917 active site 504832005918 metal binding site A [ion binding]; metal-binding site 504832005919 DNA binding site [nucleotide binding] 504832005920 putative AP binding site [nucleotide binding]; other site 504832005921 putative metal binding site B [ion binding]; other site 504832005922 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 504832005923 Sel1-like repeats; Region: SEL1; smart00671 504832005924 Sel1-like repeats; Region: SEL1; smart00671 504832005925 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 504832005926 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832005927 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 504832005928 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 504832005929 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832005930 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 504832005931 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 504832005932 E3 interaction surface; other site 504832005933 lipoyl attachment site [posttranslational modification]; other site 504832005934 e3 binding domain; Region: E3_binding; pfam02817 504832005935 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11857 504832005936 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 504832005937 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 504832005938 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 504832005939 E3 interaction surface; other site 504832005940 lipoyl attachment site [posttranslational modification]; other site 504832005941 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 504832005942 alpha subunit interface [polypeptide binding]; other site 504832005943 TPP binding site [chemical binding]; other site 504832005944 heterodimer interface [polypeptide binding]; other site 504832005945 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 504832005946 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 504832005947 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 504832005948 tetramer interface [polypeptide binding]; other site 504832005949 TPP-binding site [chemical binding]; other site 504832005950 heterodimer interface [polypeptide binding]; other site 504832005951 phosphorylation loop region [posttranslational modification] 504832005952 sulfite oxidase; Provisional; Region: PLN00177 504832005953 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 504832005954 Moco binding site; other site 504832005955 metal coordination site [ion binding]; other site 504832005956 dimerization interface [polypeptide binding]; other site 504832005957 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 504832005958 Septum formation initiator; Region: DivIC; pfam04977 504832005959 Predicted flavoprotein [General function prediction only]; Region: COG0431 504832005960 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832005961 enolase; Provisional; Region: eno; PRK00077 504832005962 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 504832005963 dimer interface [polypeptide binding]; other site 504832005964 metal binding site [ion binding]; metal-binding site 504832005965 substrate binding pocket [chemical binding]; other site 504832005966 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 504832005967 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 504832005968 Protein of unknown function (DUF497); Region: DUF497; pfam04365 504832005969 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 504832005970 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 504832005971 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 504832005972 NIPSNAP; Region: NIPSNAP; pfam07978 504832005973 Predicted periplasmic protein [Function unknown]; Region: COG3904 504832005974 CTP synthetase; Validated; Region: pyrG; PRK05380 504832005975 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 504832005976 Catalytic site [active] 504832005977 active site 504832005978 UTP binding site [chemical binding]; other site 504832005979 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 504832005980 active site 504832005981 putative oxyanion hole; other site 504832005982 catalytic triad [active] 504832005983 protein translocase, SecG subunit; Region: secG; TIGR00810 504832005984 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 504832005985 triosephosphate isomerase; Provisional; Region: PRK14565 504832005986 substrate binding site [chemical binding]; other site 504832005987 dimer interface [polypeptide binding]; other site 504832005988 catalytic triad [active] 504832005989 SurA N-terminal domain; Region: SurA_N_3; cl07813 504832005990 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 504832005991 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 504832005992 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 504832005993 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 504832005994 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 504832005995 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 504832005996 active site 504832005997 ribulose/triose binding site [chemical binding]; other site 504832005998 phosphate binding site [ion binding]; other site 504832005999 substrate (anthranilate) binding pocket [chemical binding]; other site 504832006000 product (indole) binding pocket [chemical binding]; other site 504832006001 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 504832006002 trimer interface [polypeptide binding]; other site 504832006003 dimer interface [polypeptide binding]; other site 504832006004 putative active site [active] 504832006005 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 504832006006 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 504832006007 dimer interface [polypeptide binding]; other site 504832006008 putative functional site; other site 504832006009 putative MPT binding site; other site 504832006010 LexA repressor; Validated; Region: PRK00215 504832006011 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 504832006012 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 504832006013 Catalytic site [active] 504832006014 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; pfam09923 504832006015 NADH dehydrogenase; Validated; Region: PRK08183 504832006016 BA14K-like protein; Region: BA14K; pfam07886 504832006017 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 504832006018 EamA-like transporter family; Region: EamA; pfam00892 504832006019 EamA-like transporter family; Region: EamA; pfam00892 504832006020 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 504832006021 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832006022 NAD(P) binding site [chemical binding]; other site 504832006023 active site 504832006024 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 504832006025 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 504832006026 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832006027 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006028 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 504832006029 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832006030 dimer interface [polypeptide binding]; other site 504832006031 putative CheW interface [polypeptide binding]; other site 504832006032 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 504832006033 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006034 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 504832006035 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 504832006036 hypothetical protein; Provisional; Region: PRK10756 504832006037 CreA protein; Region: CreA; pfam05981 504832006038 hypothetical protein; Provisional; Region: PRK06132 504832006039 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832006040 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 504832006041 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 504832006042 NodB motif; other site 504832006043 active site 504832006044 catalytic site [active] 504832006045 metal binding site [ion binding]; metal-binding site 504832006046 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 504832006047 Malic enzyme, N-terminal domain; Region: malic; pfam00390 504832006048 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 504832006049 putative NAD(P) binding site [chemical binding]; other site 504832006050 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 504832006051 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 504832006052 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 504832006053 dimer interface [polypeptide binding]; other site 504832006054 anticodon binding site; other site 504832006055 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 504832006056 homodimer interface [polypeptide binding]; other site 504832006057 motif 1; other site 504832006058 active site 504832006059 motif 2; other site 504832006060 GAD domain; Region: GAD; pfam02938 504832006061 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 504832006062 active site 504832006063 motif 3; other site 504832006064 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 504832006065 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 504832006066 catalytic site [active] 504832006067 putative active site [active] 504832006068 putative substrate binding site [chemical binding]; other site 504832006069 HRDC domain; Region: HRDC; pfam00570 504832006070 exopolyphosphatase; Region: exo_poly_only; TIGR03706 504832006071 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 504832006072 polyphosphate kinase; Provisional; Region: PRK05443 504832006073 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 504832006074 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 504832006075 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 504832006076 putative domain interface [polypeptide binding]; other site 504832006077 putative active site [active] 504832006078 catalytic site [active] 504832006079 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 504832006080 putative domain interface [polypeptide binding]; other site 504832006081 putative active site [active] 504832006082 catalytic site [active] 504832006083 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 504832006084 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 504832006085 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 504832006086 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 504832006087 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 504832006088 dimerization interface [polypeptide binding]; other site 504832006089 putative ATP binding site [chemical binding]; other site 504832006090 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 504832006091 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 504832006092 active site 504832006093 substrate binding site [chemical binding]; other site 504832006094 cosubstrate binding site; other site 504832006095 catalytic site [active] 504832006096 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 504832006097 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 504832006098 active site 504832006099 multimer interface [polypeptide binding]; other site 504832006100 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 504832006101 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832006102 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832006103 ABC transporter; Region: ABC_tran_2; pfam12848 504832006104 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832006105 DNA polymerase III subunit chi; Validated; Region: PRK05728 504832006106 multifunctional aminopeptidase A; Provisional; Region: PRK00913 504832006107 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 504832006108 interface (dimer of trimers) [polypeptide binding]; other site 504832006109 Substrate-binding/catalytic site; other site 504832006110 Zn-binding sites [ion binding]; other site 504832006111 Predicted permeases [General function prediction only]; Region: COG0795 504832006112 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 504832006113 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 504832006114 OstA-like protein; Region: OstA; cl00844 504832006115 Organic solvent tolerance protein; Region: OstA_C; pfam04453 504832006116 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 504832006117 SurA N-terminal domain; Region: SurA_N; pfam09312 504832006118 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK05312 504832006119 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 504832006120 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 504832006121 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 504832006122 S-adenosylmethionine binding site [chemical binding]; other site 504832006123 6-hydroxyhexanoate dehydrogenase; Region: 6_hydroxyhexanoate_dh_like; cd08240 504832006124 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 504832006125 putative NAD(P) binding site [chemical binding]; other site 504832006126 catalytic Zn binding site [ion binding]; other site 504832006127 glycoprotein BALF4; Provisional; Region: PHA03231 504832006128 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 504832006129 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 504832006130 putative catalytic residue [active] 504832006131 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 504832006132 metabolite-proton symporter; Region: 2A0106; TIGR00883 504832006133 putative substrate translocation pore; other site 504832006134 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 504832006135 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 504832006136 catalytic site [active] 504832006137 G-X2-G-X-G-K; other site 504832006138 hypothetical protein; Provisional; Region: PRK11820 504832006139 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 504832006140 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 504832006141 YceG-like family; Region: YceG; pfam02618 504832006142 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 504832006143 dimerization interface [polypeptide binding]; other site 504832006144 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 504832006145 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 504832006146 dimer interface [polypeptide binding]; other site 504832006147 active site 504832006148 acyl carrier protein; Provisional; Region: acpP; PRK00982 504832006149 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed; Region: PRK12936 504832006150 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832006151 NAD(P) binding site [chemical binding]; other site 504832006152 active site 504832006153 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 504832006154 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 504832006155 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 504832006156 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 504832006157 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 504832006158 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 504832006159 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 504832006160 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 504832006161 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 504832006162 S-adenosylmethionine binding site [chemical binding]; other site 504832006163 replicative DNA helicase; Provisional; Region: PRK09165 504832006164 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 504832006165 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 504832006166 Walker A motif; other site 504832006167 ATP binding site [chemical binding]; other site 504832006168 Walker B motif; other site 504832006169 DNA binding loops [nucleotide binding] 504832006170 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 504832006171 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 504832006172 active site 504832006173 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 504832006174 dimer interface [polypeptide binding]; other site 504832006175 substrate binding site [chemical binding]; other site 504832006176 catalytic residues [active] 504832006177 DNA repair protein RadA; Provisional; Region: PRK11823 504832006178 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 504832006179 Walker A motif; other site 504832006180 ATP binding site [chemical binding]; other site 504832006181 Walker B motif; other site 504832006182 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 504832006183 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 504832006184 Colicin V production protein; Region: Colicin_V; pfam02674 504832006185 amidophosphoribosyltransferase; Provisional; Region: PRK09123 504832006186 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 504832006187 active site 504832006188 tetramer interface [polypeptide binding]; other site 504832006189 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832006190 active site 504832006191 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 504832006192 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 504832006193 classical (c) SDRs; Region: SDR_c; cd05233 504832006194 NAD(P) binding site [chemical binding]; other site 504832006195 active site 504832006196 GTP-binding protein Der; Reviewed; Region: PRK00093 504832006197 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 504832006198 G1 box; other site 504832006199 GTP/Mg2+ binding site [chemical binding]; other site 504832006200 Switch I region; other site 504832006201 G2 box; other site 504832006202 Switch II region; other site 504832006203 G3 box; other site 504832006204 G4 box; other site 504832006205 G5 box; other site 504832006206 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 504832006207 G1 box; other site 504832006208 GTP/Mg2+ binding site [chemical binding]; other site 504832006209 Switch I region; other site 504832006210 G2 box; other site 504832006211 G3 box; other site 504832006212 Switch II region; other site 504832006213 G4 box; other site 504832006214 G5 box; other site 504832006215 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 504832006216 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 504832006217 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 504832006218 oligomerization interface [polypeptide binding]; other site 504832006219 active site 504832006220 metal binding site [ion binding]; metal-binding site 504832006221 NnrU protein; Region: NnrU; pfam07298 504832006222 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 504832006223 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 504832006224 G1 box; other site 504832006225 putative GEF interaction site [polypeptide binding]; other site 504832006226 GTP/Mg2+ binding site [chemical binding]; other site 504832006227 Switch I region; other site 504832006228 G2 box; other site 504832006229 G3 box; other site 504832006230 Switch II region; other site 504832006231 G4 box; other site 504832006232 G5 box; other site 504832006233 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 504832006234 multidrug efflux system protein; Provisional; Region: PRK11431 504832006235 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832006236 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 504832006237 TM-ABC transporter signature motif; other site 504832006238 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 504832006239 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 504832006240 TM-ABC transporter signature motif; other site 504832006241 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832006242 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832006243 Walker A/P-loop; other site 504832006244 ATP binding site [chemical binding]; other site 504832006245 Q-loop/lid; other site 504832006246 ABC transporter signature motif; other site 504832006247 Walker B; other site 504832006248 D-loop; other site 504832006249 H-loop/switch region; other site 504832006250 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832006251 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832006252 Walker A/P-loop; other site 504832006253 ATP binding site [chemical binding]; other site 504832006254 Q-loop/lid; other site 504832006255 ABC transporter signature motif; other site 504832006256 Walker B; other site 504832006257 D-loop; other site 504832006258 H-loop/switch region; other site 504832006259 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 504832006260 ArsC family; Region: ArsC; pfam03960 504832006261 putative catalytic residues [active] 504832006262 Conserved hypothetical protein (Lin0512_fam); Region: Lin0512_fam; cl09807 504832006263 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cl02915 504832006264 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 504832006265 Cl- selectivity filter; other site 504832006266 Cl- binding residues [ion binding]; other site 504832006267 pore gating glutamate residue; other site 504832006268 dimer interface [polypeptide binding]; other site 504832006269 TIR domain; Region: TIR_2; pfam13676 504832006270 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 504832006271 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 504832006272 active site 504832006273 catalytic site [active] 504832006274 substrate binding site [chemical binding]; other site 504832006275 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 504832006276 Walker A motif; other site 504832006277 ATP binding site [chemical binding]; other site 504832006278 Walker B motif; other site 504832006279 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 504832006280 active site 504832006281 NTP binding site [chemical binding]; other site 504832006282 metal binding triad [ion binding]; metal-binding site 504832006283 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 504832006284 non-specific DNA binding site [nucleotide binding]; other site 504832006285 salt bridge; other site 504832006286 sequence-specific DNA binding site [nucleotide binding]; other site 504832006287 Domain of unknown function (DUF955); Region: DUF955; cl01076 504832006288 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 504832006289 active site 504832006290 catalytic triad [active] 504832006291 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 504832006292 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 504832006293 Walker A motif; other site 504832006294 ATP binding site [chemical binding]; other site 504832006295 Walker B motif; other site 504832006296 arginine finger; other site 504832006297 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 504832006298 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 504832006299 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 504832006300 VirB7 interaction site; other site 504832006301 conjugal transfer protein TrbF; Provisional; Region: PRK13872 504832006302 conjugal transfer protein TrbL; Provisional; Region: PRK13875 504832006303 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 504832006304 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 504832006305 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 504832006306 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 504832006307 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832006308 Walker A/P-loop; other site 504832006309 ATP binding site [chemical binding]; other site 504832006310 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832006311 Walker B; other site 504832006312 D-loop; other site 504832006313 H-loop/switch region; other site 504832006314 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 504832006315 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 504832006316 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 504832006317 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 504832006318 ATP binding site [chemical binding]; other site 504832006319 Walker A motif; other site 504832006320 hexamer interface [polypeptide binding]; other site 504832006321 Walker B motif; other site 504832006322 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832006323 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832006324 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 504832006325 dimerization interface [polypeptide binding]; other site 504832006326 substrate binding pocket [chemical binding]; other site 504832006327 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 504832006328 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 504832006329 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 504832006330 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 504832006331 metal-binding site [ion binding] 504832006332 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832006333 Soluble P-type ATPase [General function prediction only]; Region: COG4087 504832006334 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 504832006335 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 504832006336 lipoyl-biotinyl attachment site [posttranslational modification]; other site 504832006337 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006338 Outer membrane efflux protein; Region: OEP; pfam02321 504832006339 Outer membrane efflux protein; Region: OEP; pfam02321 504832006340 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 504832006341 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 504832006342 Walker A motif; other site 504832006343 ATP binding site [chemical binding]; other site 504832006344 Walker B motif; other site 504832006345 Putative transcription activator [Transcription]; Region: TenA; COG0819 504832006346 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 504832006347 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 504832006348 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832006349 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 504832006350 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832006351 catalytic residue [active] 504832006352 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832006353 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 504832006354 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 504832006355 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 504832006356 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 504832006357 DNA methylase; Region: N6_N4_Mtase; pfam01555 504832006358 Replication initiator protein A; Region: RPA; pfam10134 504832006359 Helix-turn-helix domain; Region: HTH_17; pfam12728 504832006360 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 504832006361 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 504832006362 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832006363 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 504832006364 non-specific DNA binding site [nucleotide binding]; other site 504832006365 salt bridge; other site 504832006366 sequence-specific DNA binding site [nucleotide binding]; other site 504832006367 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832006368 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 504832006369 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 504832006370 integrase; Provisional; Region: PRK09692 504832006371 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 504832006372 active site 504832006373 Int/Topo IB signature motif; other site 504832006374 GMP synthase; Reviewed; Region: guaA; PRK00074 504832006375 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 504832006376 AMP/PPi binding site [chemical binding]; other site 504832006377 candidate oxyanion hole; other site 504832006378 catalytic triad [active] 504832006379 potential glutamine specificity residues [chemical binding]; other site 504832006380 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 504832006381 ATP Binding subdomain [chemical binding]; other site 504832006382 Ligand Binding sites [chemical binding]; other site 504832006383 Dimerization subdomain; other site 504832006384 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 504832006385 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 504832006386 MAPEG family; Region: MAPEG; cl09190 504832006387 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 504832006388 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 504832006389 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 504832006390 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 504832006391 active site 504832006392 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 504832006393 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832006394 putative substrate translocation pore; other site 504832006395 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 504832006396 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 504832006397 S-adenosylmethionine binding site [chemical binding]; other site 504832006398 exopolyphosphatase; Region: exo_poly_only; TIGR03706 504832006399 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 504832006400 hypothetical protein; Validated; Region: PRK00124 504832006401 ABC transporter ATPase component; Reviewed; Region: PRK11147 504832006402 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832006403 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832006404 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832006405 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832006406 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 504832006407 dimerization interface [polypeptide binding]; other site 504832006408 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 504832006409 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 504832006410 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832006411 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 504832006412 putative ligand binding site [chemical binding]; other site 504832006413 hypothetical protein; Provisional; Region: PRK07236 504832006414 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 504832006415 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 504832006416 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 504832006417 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 504832006418 putative substrate translocation pore; other site 504832006419 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832006420 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 504832006421 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 504832006422 dimer interface [polypeptide binding]; other site 504832006423 active site 504832006424 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 504832006425 Protein export membrane protein; Region: SecD_SecF; cl14618 504832006426 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 504832006427 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832006428 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006429 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 504832006430 MarR family; Region: MarR; pfam01047 504832006431 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 504832006432 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 504832006433 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 504832006434 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 504832006435 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 504832006436 N-terminal plug; other site 504832006437 ligand-binding site [chemical binding]; other site 504832006438 PilZ domain; Region: PilZ; pfam07238 504832006439 Domain of unknown function DUF87; Region: DUF87; pfam01935 504832006440 HerA helicase [Replication, recombination, and repair]; Region: COG0433 504832006441 acyl carrier protein; Provisional; Region: PRK06508 504832006442 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 504832006443 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06519 504832006444 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 504832006445 active site 504832006446 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06501 504832006447 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 504832006448 dimer interface [polypeptide binding]; other site 504832006449 active site 504832006450 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 504832006451 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 504832006452 putative NAD(P) binding site [chemical binding]; other site 504832006453 structural Zn binding site [ion binding]; other site 504832006454 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 504832006455 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 504832006456 putative acyl-acceptor binding pocket; other site 504832006457 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 504832006458 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 504832006459 hypothetical protein; Provisional; Region: PRK08912 504832006460 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 504832006461 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832006462 homodimer interface [polypeptide binding]; other site 504832006463 catalytic residue [active] 504832006464 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 504832006465 active site residue [active] 504832006466 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 504832006467 potassium uptake protein; Region: kup; TIGR00794 504832006468 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 504832006469 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 504832006470 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 504832006471 ligand binding site [chemical binding]; other site 504832006472 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 504832006473 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 504832006474 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 504832006475 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 504832006476 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 504832006477 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832006478 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 504832006479 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 504832006480 Walker A/P-loop; other site 504832006481 ATP binding site [chemical binding]; other site 504832006482 Q-loop/lid; other site 504832006483 ABC transporter signature motif; other site 504832006484 Walker B; other site 504832006485 D-loop; other site 504832006486 H-loop/switch region; other site 504832006487 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 504832006488 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 504832006489 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 504832006490 active site 504832006491 catalytic residues [active] 504832006492 metal binding site [ion binding]; metal-binding site 504832006493 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 504832006494 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 504832006495 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832006496 Coenzyme A binding pocket [chemical binding]; other site 504832006497 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 504832006498 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 504832006499 active site 504832006500 HIGH motif; other site 504832006501 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 504832006502 KMSKS motif; other site 504832006503 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 504832006504 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 504832006505 NAD synthetase; Provisional; Region: PRK13981 504832006506 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 504832006507 multimer interface [polypeptide binding]; other site 504832006508 active site 504832006509 catalytic triad [active] 504832006510 protein interface 1 [polypeptide binding]; other site 504832006511 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 504832006512 homodimer interface [polypeptide binding]; other site 504832006513 NAD binding pocket [chemical binding]; other site 504832006514 ATP binding pocket [chemical binding]; other site 504832006515 Mg binding site [ion binding]; other site 504832006516 active-site loop [active] 504832006517 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 504832006518 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 504832006519 Uncharacterized conserved protein [Function unknown]; Region: COG3391 504832006520 glutathione reductase; Validated; Region: PRK06116 504832006521 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832006522 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832006523 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 504832006524 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 504832006525 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 504832006526 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832006527 active site 504832006528 dimer interface [polypeptide binding]; other site 504832006529 phosphoglycolate phosphatase; Provisional; Region: PRK13222 504832006530 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 504832006531 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 504832006532 motif II; other site 504832006533 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 504832006534 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 504832006535 FeS/SAM binding site; other site 504832006536 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 504832006537 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 504832006538 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 504832006539 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 504832006540 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 504832006541 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 504832006542 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 504832006543 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 504832006544 Domain of unknown function DUF59; Region: DUF59; pfam01883 504832006545 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 504832006546 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 504832006547 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 504832006548 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 504832006549 putative Mg(2+) transport ATPase; Provisional; Region: PRK09977 504832006550 MgtC family; Region: MgtC; pfam02308 504832006551 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832006552 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 504832006553 dimer interface [polypeptide binding]; other site 504832006554 phosphorylation site [posttranslational modification] 504832006555 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 504832006556 ATP binding site [chemical binding]; other site 504832006557 Mg2+ binding site [ion binding]; other site 504832006558 G-X-G motif; other site 504832006559 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 504832006560 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 504832006561 catalytic motif [active] 504832006562 Catalytic residue [active] 504832006563 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 504832006564 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 504832006565 FMN binding site [chemical binding]; other site 504832006566 active site 504832006567 catalytic residues [active] 504832006568 substrate binding site [chemical binding]; other site 504832006569 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 504832006570 Transcriptional regulators [Transcription]; Region: MarR; COG1846 504832006571 MarR family; Region: MarR; pfam01047 504832006572 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 504832006573 formyl-coenzyme A transferase; Provisional; Region: PRK05398 504832006574 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832006575 putative oxalyl-CoA decarboxylase; Validated; Region: PRK09259 504832006576 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 504832006577 PYR/PP interface [polypeptide binding]; other site 504832006578 dimer interface [polypeptide binding]; other site 504832006579 TPP binding site [chemical binding]; other site 504832006580 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 504832006581 Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL...; Region: TPP_BZL_OCoD_HPCL; cd02004 504832006582 TPP-binding site; other site 504832006583 dimer interface [polypeptide binding]; other site 504832006584 oxalate/formate antiporter; Region: oxa_formateAnti; TIGR04259 504832006585 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 504832006586 putative substrate translocation pore; other site 504832006587 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 504832006588 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 504832006589 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 504832006590 CoA binding domain; Region: CoA_binding_2; pfam13380 504832006591 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 504832006592 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 504832006593 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 504832006594 CoA-ligase; Region: Ligase_CoA; pfam00549 504832006595 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 504832006596 CoA binding domain; Region: CoA_binding; pfam02629 504832006597 CoA-ligase; Region: Ligase_CoA; pfam00549 504832006598 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832006599 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832006600 DNA-binding site [nucleotide binding]; DNA binding site 504832006601 FCD domain; Region: FCD; pfam07729 504832006602 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 504832006603 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 504832006604 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 504832006605 pyruvate kinase; Provisional; Region: PRK06247 504832006606 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 504832006607 domain interfaces; other site 504832006608 active site 504832006609 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 504832006610 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832006611 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 504832006612 tartronate semialdehyde reductase; Provisional; Region: PRK15059 504832006613 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 504832006614 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 504832006615 glyoxylate carboligase; Provisional; Region: PRK11269 504832006616 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 504832006617 PYR/PP interface [polypeptide binding]; other site 504832006618 dimer interface [polypeptide binding]; other site 504832006619 TPP binding site [chemical binding]; other site 504832006620 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 504832006621 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 504832006622 TPP-binding site [chemical binding]; other site 504832006623 transcriptional repressor IclR; Provisional; Region: PRK11569 504832006624 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 504832006625 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832006626 Uncharacterized conserved protein [Function unknown]; Region: COG3791 504832006627 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 504832006628 CoA binding domain; Region: CoA_binding; pfam02629 504832006629 CoA-ligase; Region: Ligase_CoA; pfam00549 504832006630 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 504832006631 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 504832006632 CoA-ligase; Region: Ligase_CoA; pfam00549 504832006633 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 504832006634 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 504832006635 metal binding triad; other site 504832006636 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 504832006637 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 504832006638 metal binding triad; other site 504832006639 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 504832006640 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832006641 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 504832006642 dimerization interface [polypeptide binding]; other site 504832006643 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 504832006644 dimer interface [polypeptide binding]; other site 504832006645 phosphorylation site [posttranslational modification] 504832006646 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 504832006647 ATP binding site [chemical binding]; other site 504832006648 Mg2+ binding site [ion binding]; other site 504832006649 G-X-G motif; other site 504832006650 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832006651 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832006652 active site 504832006653 phosphorylation site [posttranslational modification] 504832006654 intermolecular recognition site; other site 504832006655 dimerization interface [polypeptide binding]; other site 504832006656 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 504832006657 DNA binding site [nucleotide binding] 504832006658 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 504832006659 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 504832006660 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 504832006661 protein binding site [polypeptide binding]; other site 504832006662 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 504832006663 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 504832006664 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 504832006665 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 504832006666 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 504832006667 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 504832006668 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 504832006669 binding surface 504832006670 TPR motif; other site 504832006671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832006672 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 504832006673 ATP binding site [chemical binding]; other site 504832006674 Mg2+ binding site [ion binding]; other site 504832006675 G-X-G motif; other site 504832006676 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832006677 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832006678 active site 504832006679 phosphorylation site [posttranslational modification] 504832006680 intermolecular recognition site; other site 504832006681 dimerization interface [polypeptide binding]; other site 504832006682 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 504832006683 DNA binding site [nucleotide binding] 504832006684 PilZ domain; Region: PilZ; pfam07238 504832006685 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 504832006686 catalytic residues [active] 504832006687 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 504832006688 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 504832006689 putative trimer interface [polypeptide binding]; other site 504832006690 putative CoA binding site [chemical binding]; other site 504832006691 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 504832006692 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 504832006693 Putative phage tail protein; Region: Phage-tail_3; pfam13550 504832006694 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 504832006695 putative phage cell wall peptidase, NlpC/P60 family; Region: phage_NlpC_fam; TIGR02219 504832006696 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 504832006697 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 504832006698 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 504832006699 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 504832006700 Phage-related minor tail protein [Function unknown]; Region: COG5281 504832006701 phage conserved hypothetical protein; Region: phage_TIGR02216 504832006702 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 504832006703 Phage major tail protein 2; Region: Phage_tail_2; cl11463 504832006704 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 504832006705 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 504832006706 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 504832006707 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 504832006708 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 504832006709 oligomerization interface [polypeptide binding]; other site 504832006710 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 504832006711 active site 504832006712 substrate binding sites [chemical binding]; other site 504832006713 Porin subfamily; Region: Porin_2; pfam02530 504832006714 PilZ domain; Region: PilZ; cl01260 504832006715 Domain of unknown function (DUF2019); Region: DUF2019; pfam09450 504832006716 Predicted phage phi-C31 gp36 major capsid-like protein [General function prediction only]; Region: COG4653 504832006717 Phage capsid family; Region: Phage_capsid; pfam05065 504832006718 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 504832006719 Phage-related protein [Function unknown]; Region: COG4695 504832006720 Phage portal protein; Region: Phage_portal; pfam04860 504832006721 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 504832006722 GIY-YIG motif/motif A; other site 504832006723 putative active site [active] 504832006724 putative metal binding site [ion binding]; other site 504832006725 Uncharacterized conserved protein [Function unknown]; Region: COG5323 504832006726 Terminase-like family; Region: Terminase_6; pfam03237 504832006727 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 504832006728 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832006729 putative substrate translocation pore; other site 504832006730 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 504832006731 hypothetical protein; Provisional; Region: PRK05170 504832006732 Transglycosylase; Region: Transgly; pfam00912 504832006733 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 504832006734 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 504832006735 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 504832006736 Predicted integral membrane protein [Function unknown]; Region: COG5436 504832006737 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 504832006738 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 504832006739 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 504832006740 Protein of unknown function (DUF1491); Region: DUF1491; pfam07372 504832006741 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832006742 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 504832006743 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 504832006744 putative active site [active] 504832006745 heme pocket [chemical binding]; other site 504832006746 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 504832006747 dimer interface [polypeptide binding]; other site 504832006748 phosphorylation site [posttranslational modification] 504832006749 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 504832006750 ATP binding site [chemical binding]; other site 504832006751 Mg2+ binding site [ion binding]; other site 504832006752 G-X-G motif; other site 504832006753 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 504832006754 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 504832006755 hypothetical protein; Validated; Region: PRK09104 504832006756 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 504832006757 metal binding site [ion binding]; metal-binding site 504832006758 putative dimer interface [polypeptide binding]; other site 504832006759 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 504832006760 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 504832006761 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 504832006762 dihydropteroate synthase; Region: DHPS; TIGR01496 504832006763 substrate binding pocket [chemical binding]; other site 504832006764 dimer interface [polypeptide binding]; other site 504832006765 inhibitor binding site; inhibition site 504832006766 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 504832006767 homooctamer interface [polypeptide binding]; other site 504832006768 active site 504832006769 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 504832006770 catalytic center binding site [active] 504832006771 ATP binding site [chemical binding]; other site 504832006772 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 504832006773 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; cl00237 504832006774 putative substrate binding pocket [chemical binding]; other site 504832006775 AC domain interface; other site 504832006776 catalytic triad [active] 504832006777 AB domain interface; other site 504832006778 twin-arg-translocated uncharacterized repeat protein; Region: RR_plus_rpt_1; TIGR03808 504832006779 TIGR03809 family protein; Region: TIGR03809 504832006780 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832006781 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832006782 metal binding site [ion binding]; metal-binding site 504832006783 active site 504832006784 I-site; other site 504832006785 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 504832006786 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 504832006787 RNA polymerase sigma factor; Provisional; Region: PRK12536 504832006788 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832006789 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 504832006790 DNA binding residues [nucleotide binding] 504832006791 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 504832006792 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 504832006793 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 504832006794 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 504832006795 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 504832006796 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 504832006797 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006798 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 504832006799 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 504832006800 metal binding site [ion binding]; metal-binding site 504832006801 putative dimer interface [polypeptide binding]; other site 504832006802 choline dehydrogenase; Validated; Region: PRK02106 504832006803 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 504832006804 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 504832006805 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 504832006806 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 504832006807 inhibitor-cofactor binding pocket; inhibition site 504832006808 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832006809 catalytic residue [active] 504832006810 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 504832006811 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 504832006812 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 504832006813 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 504832006814 TPP-binding site; other site 504832006815 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 504832006816 PYR/PP interface [polypeptide binding]; other site 504832006817 dimer interface [polypeptide binding]; other site 504832006818 TPP binding site [chemical binding]; other site 504832006819 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 504832006820 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 504832006821 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 504832006822 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 504832006823 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 504832006824 FeS/SAM binding site; other site 504832006825 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 504832006826 Methyltransferase domain; Region: Methyltransf_24; pfam13578 504832006827 hypothetical protein; Provisional; Region: PRK07077 504832006828 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 504832006829 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 504832006830 Active site cavity [active] 504832006831 catalytic acid [active] 504832006832 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 504832006833 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 504832006834 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 504832006835 active site lid residues [active] 504832006836 substrate binding pocket [chemical binding]; other site 504832006837 catalytic residues [active] 504832006838 substrate-Mg2+ binding site; other site 504832006839 aspartate-rich region 1; other site 504832006840 aspartate-rich region 2; other site 504832006841 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 504832006842 active site lid residues [active] 504832006843 substrate binding pocket [chemical binding]; other site 504832006844 catalytic residues [active] 504832006845 substrate-Mg2+ binding site; other site 504832006846 aspartate-rich region 1; other site 504832006847 aspartate-rich region 2; other site 504832006848 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 504832006849 B12 binding domain; Region: B12-binding; pfam02310 504832006850 B12 binding site [chemical binding]; other site 504832006851 Domain of unknown function (DUF4070); Region: DUF4070; pfam13282 504832006852 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 504832006853 rhodanese superfamily protein; Provisional; Region: PRK05320 504832006854 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 504832006855 active site residue [active] 504832006856 SlyX; Region: SlyX; pfam04102 504832006857 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 504832006858 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 504832006859 active site 504832006860 catalytic tetrad [active] 504832006861 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 504832006862 FecR protein; Region: FecR; pfam04773 504832006863 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 504832006864 binding surface 504832006865 Tetratricopeptide repeat; Region: TPR_16; pfam13432 504832006866 TPR motif; other site 504832006867 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 504832006868 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 504832006869 multidrug efflux protein; Reviewed; Region: PRK09579 504832006870 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 504832006871 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832006872 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832006873 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832006874 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832006875 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832006876 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832006877 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 504832006878 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 504832006879 homodimer interface [polypeptide binding]; other site 504832006880 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832006881 catalytic residue [active] 504832006882 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832006883 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 504832006884 homodimer interface [polypeptide binding]; other site 504832006885 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832006886 catalytic residue [active] 504832006887 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832006888 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832006889 DNA-binding site [nucleotide binding]; DNA binding site 504832006890 FCD domain; Region: FCD; pfam07729 504832006891 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 504832006892 FAD binding domain; Region: FAD_binding_4; pfam01565 504832006893 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 504832006894 Domain of unknown function (DUF336); Region: DUF336; cl01249 504832006895 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832006896 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832006897 enoyl-CoA hydratase; Provisional; Region: PRK06127 504832006898 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 504832006899 substrate binding site [chemical binding]; other site 504832006900 oxyanion hole (OAH) forming residues; other site 504832006901 trimer interface [polypeptide binding]; other site 504832006902 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 504832006903 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 504832006904 dimer interface [polypeptide binding]; other site 504832006905 active site 504832006906 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 504832006907 substrate binding site [chemical binding]; other site 504832006908 catalytic residue [active] 504832006909 allantoate amidohydrolase; Reviewed; Region: PRK09290 504832006910 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 504832006911 active site 504832006912 metal binding site [ion binding]; metal-binding site 504832006913 dimer interface [polypeptide binding]; other site 504832006914 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 504832006915 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 504832006916 catalytic loop [active] 504832006917 iron binding site [ion binding]; other site 504832006918 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 504832006919 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 504832006920 [4Fe-4S] binding site [ion binding]; other site 504832006921 molybdopterin cofactor binding site; other site 504832006922 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 504832006923 molybdopterin cofactor binding site; other site 504832006924 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 504832006925 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 504832006926 putative dimer interface [polypeptide binding]; other site 504832006927 [2Fe-2S] cluster binding site [ion binding]; other site 504832006928 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 504832006929 SLBB domain; Region: SLBB; pfam10531 504832006930 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 504832006931 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 504832006932 ArsC family; Region: ArsC; pfam03960 504832006933 catalytic residues [active] 504832006934 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 504832006935 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832006936 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 504832006937 Walker A/P-loop; other site 504832006938 ATP binding site [chemical binding]; other site 504832006939 Q-loop/lid; other site 504832006940 ABC transporter signature motif; other site 504832006941 Walker B; other site 504832006942 D-loop; other site 504832006943 H-loop/switch region; other site 504832006944 PBP superfamily domain; Region: PBP_like_2; pfam12849 504832006945 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 504832006946 beta-lactamase TEM; Provisional; Region: PRK15442 504832006947 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 504832006948 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 504832006949 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 504832006950 putative substrate translocation pore; other site 504832006951 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 504832006952 CPxP motif; other site 504832006953 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 504832006954 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 504832006955 dimer interface [polypeptide binding]; other site 504832006956 putative functional site; other site 504832006957 putative MPT binding site; other site 504832006958 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 504832006959 Walker A motif; other site 504832006960 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 504832006961 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 504832006962 GTP binding site; other site 504832006963 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional; Region: PRK14498 504832006964 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 504832006965 dimer interface [polypeptide binding]; other site 504832006966 putative functional site; other site 504832006967 putative MPT binding site; other site 504832006968 PBP superfamily domain; Region: PBP_like; pfam12727 504832006969 MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin; Region: MoCF_BD; cl00451 504832006970 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 504832006971 MPT binding site; other site 504832006972 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832006973 Ku-homolog [Replication, recombination, and repair]; Region: COG1273 504832006974 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 504832006975 putative DNA binding site [nucleotide binding]; other site 504832006976 putative homodimer interface [polypeptide binding]; other site 504832006977 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 504832006978 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 504832006979 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 504832006980 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 504832006981 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 504832006982 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 504832006983 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 504832006984 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 504832006985 N-terminal plug; other site 504832006986 ligand-binding site [chemical binding]; other site 504832006987 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 504832006988 hypothetical protein; Provisional; Region: PRK07505 504832006989 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832006990 catalytic residue [active] 504832006991 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 504832006992 AAA domain; Region: AAA_26; pfam13500 504832006993 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 504832006994 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 504832006995 inhibitor-cofactor binding pocket; inhibition site 504832006996 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832006997 catalytic residue [active] 504832006998 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 504832006999 dimerization interface [polypeptide binding]; other site 504832007000 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832007001 dimer interface [polypeptide binding]; other site 504832007002 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 504832007003 putative CheW interface [polypeptide binding]; other site 504832007004 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 504832007005 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 504832007006 active site 504832007007 catalytic tetrad [active] 504832007008 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 504832007009 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 504832007010 PAS fold; Region: PAS_7; pfam12860 504832007011 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832007012 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832007013 metal binding site [ion binding]; metal-binding site 504832007014 active site 504832007015 I-site; other site 504832007016 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 504832007017 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 504832007018 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 504832007019 ligand binding site [chemical binding]; other site 504832007020 flexible hinge region; other site 504832007021 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 504832007022 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 504832007023 CoA binding domain; Region: CoA_binding; pfam02629 504832007024 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 504832007025 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 504832007026 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 504832007027 CoA-ligase; Region: Ligase_CoA; pfam00549 504832007028 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 504832007029 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 504832007030 putative catalytic cysteine [active] 504832007031 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 504832007032 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 504832007033 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 504832007034 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832007035 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832007036 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 504832007037 dimerization interface [polypeptide binding]; other site 504832007038 sulfoacetaldehyde acetyltransferase; Validated; Region: PRK07525 504832007039 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 504832007040 PYR/PP interface [polypeptide binding]; other site 504832007041 dimer interface [polypeptide binding]; other site 504832007042 TPP binding site [chemical binding]; other site 504832007043 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 504832007044 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 504832007045 TPP-binding site [chemical binding]; other site 504832007046 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832007047 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 504832007048 putative DNA binding site [nucleotide binding]; other site 504832007049 putative Zn2+ binding site [ion binding]; other site 504832007050 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832007051 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 504832007052 metabolite-proton symporter; Region: 2A0106; TIGR00883 504832007053 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 504832007054 putative substrate translocation pore; other site 504832007055 choline dehydrogenase; Validated; Region: PRK02106 504832007056 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832007057 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 504832007058 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832007059 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 504832007060 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832007061 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 504832007062 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 504832007063 THF binding site; other site 504832007064 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 504832007065 substrate binding site [chemical binding]; other site 504832007066 THF binding site; other site 504832007067 zinc-binding site [ion binding]; other site 504832007068 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 504832007069 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 504832007070 ATP cone domain; Region: ATP-cone; pfam03477 504832007071 ATP cone domain; Region: ATP-cone; pfam03477 504832007072 Class I ribonucleotide reductase; Region: RNR_I; cd01679 504832007073 active site 504832007074 dimer interface [polypeptide binding]; other site 504832007075 catalytic residues [active] 504832007076 effector binding site; other site 504832007077 R2 peptide binding site; other site 504832007078 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 504832007079 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 504832007080 dimer interface [polypeptide binding]; other site 504832007081 putative radical transfer pathway; other site 504832007082 diiron center [ion binding]; other site 504832007083 tyrosyl radical; other site 504832007084 MASE1; Region: MASE1; cl17823 504832007085 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832007086 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832007087 metal binding site [ion binding]; metal-binding site 504832007088 active site 504832007089 I-site; other site 504832007090 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 504832007091 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 504832007092 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 504832007093 Glutamate binding site [chemical binding]; other site 504832007094 NAD binding site [chemical binding]; other site 504832007095 catalytic residues [active] 504832007096 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832007097 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 504832007098 DNA binding site [nucleotide binding] 504832007099 Predicted integral membrane protein [Function unknown]; Region: COG5616 504832007100 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 504832007101 TPR motif; other site 504832007102 TPR repeat; Region: TPR_11; pfam13414 504832007103 binding surface 504832007104 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 504832007105 binding surface 504832007106 TPR motif; other site 504832007107 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832007108 NADH(P)-binding; Region: NAD_binding_10; pfam13460 504832007109 NAD(P) binding site [chemical binding]; other site 504832007110 active site 504832007111 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 504832007112 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 504832007113 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 504832007114 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 504832007115 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 504832007116 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832007117 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 504832007118 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 504832007119 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 504832007120 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 504832007121 Transcriptional regulator; Region: Transcrip_reg; cl00361 504832007122 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 504832007123 active site 504832007124 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 504832007125 TSCPD domain; Region: TSCPD; pfam12637 504832007126 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832007127 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832007128 metal binding site [ion binding]; metal-binding site 504832007129 active site 504832007130 I-site; other site 504832007131 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 504832007132 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 504832007133 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 504832007134 molybdopterin cofactor binding site; other site 504832007135 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 504832007136 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 504832007137 molybdopterin cofactor binding site; other site 504832007138 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 504832007139 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 504832007140 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 504832007141 dimer interface [polypeptide binding]; other site 504832007142 conserved gate region; other site 504832007143 putative PBP binding loops; other site 504832007144 ABC-ATPase subunit interface; other site 504832007145 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 504832007146 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 504832007147 dimer interface [polypeptide binding]; other site 504832007148 conserved gate region; other site 504832007149 putative PBP binding loops; other site 504832007150 ABC-ATPase subunit interface; other site 504832007151 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 504832007152 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832007153 Walker A/P-loop; other site 504832007154 ATP binding site [chemical binding]; other site 504832007155 Q-loop/lid; other site 504832007156 ABC transporter signature motif; other site 504832007157 Walker B; other site 504832007158 D-loop; other site 504832007159 H-loop/switch region; other site 504832007160 TOBE domain; Region: TOBE_2; pfam08402 504832007161 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 504832007162 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 504832007163 Coenzyme A transferase; Region: CoA_trans; cl17247 504832007164 Coenzyme A transferase; Region: CoA_trans; cl17247 504832007165 Coenzyme A transferase; Region: CoA_trans; smart00882 504832007166 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 504832007167 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 504832007168 acyl-activating enzyme (AAE) consensus motif; other site 504832007169 AMP binding site [chemical binding]; other site 504832007170 active site 504832007171 CoA binding site [chemical binding]; other site 504832007172 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832007173 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 504832007174 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832007175 enoyl-CoA hydratase; Provisional; Region: PRK05870 504832007176 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 504832007177 substrate binding site [chemical binding]; other site 504832007178 oxyanion hole (OAH) forming residues; other site 504832007179 trimer interface [polypeptide binding]; other site 504832007180 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 504832007181 CoA-transferase family III; Region: CoA_transf_3; pfam02515 504832007182 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832007183 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 504832007184 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832007185 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 504832007186 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 504832007187 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 504832007188 NADP binding site [chemical binding]; other site 504832007189 dimer interface [polypeptide binding]; other site 504832007190 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832007191 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 504832007192 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832007193 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 504832007194 N-terminal domain interface [polypeptide binding]; other site 504832007195 dimer interface [polypeptide binding]; other site 504832007196 substrate binding pocket (H-site) [chemical binding]; other site 504832007197 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 504832007198 iron-sulfur cluster [ion binding]; other site 504832007199 [2Fe-2S] cluster binding site [ion binding]; other site 504832007200 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 504832007201 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 504832007202 catalytic loop [active] 504832007203 iron binding site [ion binding]; other site 504832007204 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 504832007205 FAD binding pocket [chemical binding]; other site 504832007206 FAD binding motif [chemical binding]; other site 504832007207 phosphate binding motif [ion binding]; other site 504832007208 beta-alpha-beta structure motif; other site 504832007209 NAD binding pocket [chemical binding]; other site 504832007210 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 504832007211 iron-sulfur cluster [ion binding]; other site 504832007212 [2Fe-2S] cluster binding site [ion binding]; other site 504832007213 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 504832007214 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 504832007215 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 504832007216 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 504832007217 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 504832007218 metal binding site [ion binding]; metal-binding site 504832007219 substrate binding pocket [chemical binding]; other site 504832007220 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832007221 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 504832007222 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832007223 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 504832007224 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 504832007225 active site 504832007226 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 504832007227 Ligand Binding Site [chemical binding]; other site 504832007228 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832007229 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832007230 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 504832007231 dimerization interface [polypeptide binding]; other site 504832007232 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832007233 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 504832007234 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832007235 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832007236 Walker A/P-loop; other site 504832007237 ATP binding site [chemical binding]; other site 504832007238 Q-loop/lid; other site 504832007239 ABC transporter signature motif; other site 504832007240 Walker B; other site 504832007241 D-loop; other site 504832007242 H-loop/switch region; other site 504832007243 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832007244 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832007245 Walker A/P-loop; other site 504832007246 ATP binding site [chemical binding]; other site 504832007247 Q-loop/lid; other site 504832007248 ABC transporter signature motif; other site 504832007249 Walker B; other site 504832007250 D-loop; other site 504832007251 H-loop/switch region; other site 504832007252 Predicted amidohydrolase [General function prediction only]; Region: COG0388 504832007253 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 504832007254 putative active site [active] 504832007255 catalytic triad [active] 504832007256 putative dimer interface [polypeptide binding]; other site 504832007257 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 504832007258 malonyl-CoA synthase; Validated; Region: PRK07514 504832007259 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 504832007260 acyl-activating enzyme (AAE) consensus motif; other site 504832007261 active site 504832007262 AMP binding site [chemical binding]; other site 504832007263 CoA binding site [chemical binding]; other site 504832007264 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 504832007265 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 504832007266 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832007267 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 504832007268 putative C-terminal domain interface [polypeptide binding]; other site 504832007269 putative GSH binding site (G-site) [chemical binding]; other site 504832007270 putative dimer interface [polypeptide binding]; other site 504832007271 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 504832007272 putative N-terminal domain interface [polypeptide binding]; other site 504832007273 putative dimer interface [polypeptide binding]; other site 504832007274 putative substrate binding pocket (H-site) [chemical binding]; other site 504832007275 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832007276 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832007277 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 504832007278 putative effector binding pocket; other site 504832007279 putative dimerization interface [polypeptide binding]; other site 504832007280 DJ-1 family protein; Region: not_thiJ; TIGR01383 504832007281 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 504832007282 conserved cys residue [active] 504832007283 transcriptional regulatory protein PtsJ; Provisional; Region: PRK15481 504832007284 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832007285 DNA-binding site [nucleotide binding]; DNA binding site 504832007286 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 504832007287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832007288 homodimer interface [polypeptide binding]; other site 504832007289 catalytic residue [active] 504832007290 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 504832007291 heme-binding site [chemical binding]; other site 504832007292 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832007293 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832007294 metal binding site [ion binding]; metal-binding site 504832007295 active site 504832007296 I-site; other site 504832007297 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 504832007298 PAS domain; Region: PAS_9; pfam13426 504832007299 putative active site [active] 504832007300 heme pocket [chemical binding]; other site 504832007301 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 504832007302 PAS domain; Region: PAS_9; pfam13426 504832007303 putative active site [active] 504832007304 heme pocket [chemical binding]; other site 504832007305 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 504832007306 PAS domain; Region: PAS_9; pfam13426 504832007307 putative active site [active] 504832007308 heme pocket [chemical binding]; other site 504832007309 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 504832007310 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832007311 dimer interface [polypeptide binding]; other site 504832007312 putative CheW interface [polypeptide binding]; other site 504832007313 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 504832007314 dimerization interface [polypeptide binding]; other site 504832007315 putative DNA binding site [nucleotide binding]; other site 504832007316 putative Zn2+ binding site [ion binding]; other site 504832007317 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 504832007318 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 504832007319 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832007320 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 504832007321 Protein export membrane protein; Region: SecD_SecF; cl14618 504832007322 Protein export membrane protein; Region: SecD_SecF; cl14618 504832007323 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 504832007324 AAA domain; Region: AAA_33; pfam13671 504832007325 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 504832007326 CoA binding domain; Region: CoA_binding_2; pfam13380 504832007327 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 504832007328 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 504832007329 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 504832007330 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832007331 Coenzyme A binding pocket [chemical binding]; other site 504832007332 putative phosphoketolase; Provisional; Region: PRK05261 504832007333 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 504832007334 TPP-binding site; other site 504832007335 XFP C-terminal domain; Region: XFP_C; pfam09363 504832007336 FOG: CBS domain [General function prediction only]; Region: COG0517 504832007337 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 504832007338 FOG: CBS domain [General function prediction only]; Region: COG0517 504832007339 BON domain; Region: BON; pfam04972 504832007340 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 504832007341 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 504832007342 putative NAD(P) binding site [chemical binding]; other site 504832007343 putative substrate binding site [chemical binding]; other site 504832007344 catalytic Zn binding site [ion binding]; other site 504832007345 structural Zn binding site [ion binding]; other site 504832007346 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 504832007347 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 504832007348 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 504832007349 anti sigma factor interaction site; other site 504832007350 regulatory phosphorylation site [posttranslational modification]; other site 504832007351 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 504832007352 Permease; Region: Permease; pfam02405 504832007353 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 504832007354 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 504832007355 Walker A/P-loop; other site 504832007356 ATP binding site [chemical binding]; other site 504832007357 Q-loop/lid; other site 504832007358 ABC transporter signature motif; other site 504832007359 Walker B; other site 504832007360 D-loop; other site 504832007361 H-loop/switch region; other site 504832007362 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 504832007363 mce related protein; Region: MCE; pfam02470 504832007364 Protein of unknown function (DUF330); Region: DUF330; cl01135 504832007365 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 504832007366 Ligand Binding Site [chemical binding]; other site 504832007367 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 504832007368 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 504832007369 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 504832007370 active site 504832007371 SAM binding site [chemical binding]; other site 504832007372 homodimer interface [polypeptide binding]; other site 504832007373 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 504832007374 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 504832007375 [4Fe-4S] binding site [ion binding]; other site 504832007376 molybdopterin cofactor binding site; other site 504832007377 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 504832007378 molybdopterin cofactor binding site; other site 504832007379 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 504832007380 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 504832007381 [2Fe-2S] cluster binding site [ion binding]; other site 504832007382 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 504832007383 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832007384 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 504832007385 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 504832007386 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 504832007387 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 504832007388 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 504832007389 putative substrate translocation pore; other site 504832007390 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 504832007391 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 504832007392 active site 504832007393 phosphorylation site [posttranslational modification] 504832007394 intermolecular recognition site; other site 504832007395 ANTAR domain; Region: ANTAR; pfam03861 504832007396 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 504832007397 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 504832007398 FOG: CBS domain [General function prediction only]; Region: COG0517 504832007399 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 504832007400 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 504832007401 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 504832007402 Walker A/P-loop; other site 504832007403 ATP binding site [chemical binding]; other site 504832007404 Q-loop/lid; other site 504832007405 ABC transporter signature motif; other site 504832007406 Walker B; other site 504832007407 D-loop; other site 504832007408 H-loop/switch region; other site 504832007409 putative PBP binding regions; other site 504832007410 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 504832007411 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 504832007412 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 504832007413 ABC-ATPase subunit interface; other site 504832007414 dimer interface [polypeptide binding]; other site 504832007415 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 504832007416 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 504832007417 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832007418 Walker A/P-loop; other site 504832007419 ATP binding site [chemical binding]; other site 504832007420 Q-loop/lid; other site 504832007421 ABC transporter signature motif; other site 504832007422 Walker B; other site 504832007423 D-loop; other site 504832007424 H-loop/switch region; other site 504832007425 TOBE domain; Region: TOBE_2; pfam08402 504832007426 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 504832007427 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 504832007428 dimer interface [polypeptide binding]; other site 504832007429 conserved gate region; other site 504832007430 putative PBP binding loops; other site 504832007431 ABC-ATPase subunit interface; other site 504832007432 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 504832007433 dimer interface [polypeptide binding]; other site 504832007434 conserved gate region; other site 504832007435 putative PBP binding loops; other site 504832007436 ABC-ATPase subunit interface; other site 504832007437 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 504832007438 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 504832007439 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 504832007440 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 504832007441 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832007442 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832007443 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 504832007444 dimerization interface [polypeptide binding]; other site 504832007445 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 504832007446 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 504832007447 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832007448 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832007449 DNA-binding site [nucleotide binding]; DNA binding site 504832007450 FCD domain; Region: FCD; pfam07729 504832007451 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 504832007452 Class III alcohol dehydrogenase; Region: Zn_ADH_class_III; cd08279 504832007453 NAD binding site [chemical binding]; other site 504832007454 catalytic Zn binding site [ion binding]; other site 504832007455 substrate binding site [chemical binding]; other site 504832007456 structural Zn binding site [ion binding]; other site 504832007457 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832007458 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832007459 Walker A/P-loop; other site 504832007460 ATP binding site [chemical binding]; other site 504832007461 Q-loop/lid; other site 504832007462 ABC transporter signature motif; other site 504832007463 Walker B; other site 504832007464 D-loop; other site 504832007465 H-loop/switch region; other site 504832007466 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832007467 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832007468 Walker A/P-loop; other site 504832007469 ATP binding site [chemical binding]; other site 504832007470 Q-loop/lid; other site 504832007471 ABC transporter signature motif; other site 504832007472 Walker B; other site 504832007473 D-loop; other site 504832007474 H-loop/switch region; other site 504832007475 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832007476 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 504832007477 TM-ABC transporter signature motif; other site 504832007478 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 504832007479 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 504832007480 TM-ABC transporter signature motif; other site 504832007481 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832007482 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 504832007483 putative ligand binding site [chemical binding]; other site 504832007484 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 504832007485 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 504832007486 triphosphoribosyl-dephospho-CoA synthase MdcB; Region: malonate_mdcB; TIGR03132 504832007487 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 504832007488 malonate decarboxylase holo-[acyl-carrier-protein] synthase; Region: malonate_mdcG; TIGR03135 504832007489 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 504832007490 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 504832007491 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 504832007492 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 504832007493 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832007494 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832007495 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 504832007496 Uncharacterized conserved protein [Function unknown]; Region: COG2128 504832007497 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 504832007498 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 504832007499 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 504832007500 active site 504832007501 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832007502 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832007503 Walker A/P-loop; other site 504832007504 ATP binding site [chemical binding]; other site 504832007505 Q-loop/lid; other site 504832007506 ABC transporter signature motif; other site 504832007507 Walker B; other site 504832007508 D-loop; other site 504832007509 H-loop/switch region; other site 504832007510 NMT1-like family; Region: NMT1_2; pfam13379 504832007511 NMT1/THI5 like; Region: NMT1; pfam09084 504832007512 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832007513 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 504832007514 dimer interface [polypeptide binding]; other site 504832007515 conserved gate region; other site 504832007516 putative PBP binding loops; other site 504832007517 ABC-ATPase subunit interface; other site 504832007518 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832007519 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832007520 Cytochrome c2 [Energy production and conversion]; Region: COG3474 504832007521 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 504832007522 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 504832007523 catalytic triad [active] 504832007524 PAS fold; Region: PAS_7; pfam12860 504832007525 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832007526 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832007527 metal binding site [ion binding]; metal-binding site 504832007528 active site 504832007529 I-site; other site 504832007530 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 504832007531 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 504832007532 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 504832007533 tetrameric interface [polypeptide binding]; other site 504832007534 NAD binding site [chemical binding]; other site 504832007535 catalytic residues [active] 504832007536 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832007537 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832007538 LysR substrate binding domain; Region: LysR_substrate; pfam03466 504832007539 dimerization interface [polypeptide binding]; other site 504832007540 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 504832007541 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 504832007542 active site 504832007543 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 504832007544 enoyl-CoA hydratase; Provisional; Region: PRK06688 504832007545 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 504832007546 substrate binding site [chemical binding]; other site 504832007547 oxyanion hole (OAH) forming residues; other site 504832007548 trimer interface [polypeptide binding]; other site 504832007549 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 504832007550 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 504832007551 putative active site [active] 504832007552 Zn binding site [ion binding]; other site 504832007553 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 504832007554 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 504832007555 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 504832007556 TPP-binding site; other site 504832007557 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 504832007558 PYR/PP interface [polypeptide binding]; other site 504832007559 dimer interface [polypeptide binding]; other site 504832007560 TPP binding site [chemical binding]; other site 504832007561 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 504832007562 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 504832007563 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 504832007564 RNA binding surface [nucleotide binding]; other site 504832007565 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 504832007566 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 504832007567 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 504832007568 S-adenosylmethionine binding site [chemical binding]; other site 504832007569 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 504832007570 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 504832007571 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832007572 dimer interface [polypeptide binding]; other site 504832007573 putative CheW interface [polypeptide binding]; other site 504832007574 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 504832007575 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 504832007576 Tetramer interface [polypeptide binding]; other site 504832007577 active site 504832007578 FMN-binding site [chemical binding]; other site 504832007579 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 504832007580 catalytic core [active] 504832007581 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 504832007582 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 504832007583 NAD binding site [chemical binding]; other site 504832007584 homotetramer interface [polypeptide binding]; other site 504832007585 homodimer interface [polypeptide binding]; other site 504832007586 substrate binding site [chemical binding]; other site 504832007587 active site 504832007588 RNA polymerase sigma factor; Provisional; Region: PRK12511 504832007589 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832007590 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 504832007591 DNA binding residues [nucleotide binding] 504832007592 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 504832007593 PRC-barrel domain; Region: PRC; pfam05239 504832007594 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 504832007595 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 504832007596 HSP70 interaction site [polypeptide binding]; other site 504832007597 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 504832007598 substrate binding site [polypeptide binding]; other site 504832007599 dimer interface [polypeptide binding]; other site 504832007600 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 504832007601 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 504832007602 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 504832007603 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 504832007604 classical (c) SDRs; Region: SDR_c; cd05233 504832007605 NAD(P) binding site [chemical binding]; other site 504832007606 active site 504832007607 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 504832007608 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 504832007609 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 504832007610 active site 504832007611 DNA binding site [nucleotide binding] 504832007612 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 504832007613 DNA binding site [nucleotide binding] 504832007614 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 504832007615 nucleotide binding site [chemical binding]; other site 504832007616 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 504832007617 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 504832007618 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 504832007619 Cl binding site [ion binding]; other site 504832007620 oligomer interface [polypeptide binding]; other site 504832007621 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832007622 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832007623 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 504832007624 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832007625 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 504832007626 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 504832007627 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 504832007628 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 504832007629 FAD binding site [chemical binding]; other site 504832007630 substrate binding pocket [chemical binding]; other site 504832007631 catalytic base [active] 504832007632 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 504832007633 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 504832007634 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 504832007635 dimerization interface [polypeptide binding]; other site 504832007636 active site 504832007637 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 504832007638 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 504832007639 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 504832007640 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 504832007641 FAD binding domain; Region: FAD_binding_4; pfam01565 504832007642 Uncharacterized conserved protein [Function unknown]; Region: COG2135 504832007643 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 504832007644 nudix motif; other site 504832007645 Protein of unknown function (DUF2385); Region: DUF2385; pfam09539 504832007646 dihydroorotase; Validated; Region: PRK09060 504832007647 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 504832007648 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 504832007649 active site 504832007650 Aminomethyltransferase folate-binding domain; Region: GCV_T; pfam01571 504832007651 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 504832007652 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 504832007653 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 504832007654 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG5350 504832007655 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 504832007656 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 504832007657 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 504832007658 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 504832007659 NADP binding site [chemical binding]; other site 504832007660 dimer interface [polypeptide binding]; other site 504832007661 quinolinate synthetase; Provisional; Region: PRK09375 504832007662 L-aspartate oxidase; Provisional; Region: PRK07512 504832007663 L-aspartate oxidase; Provisional; Region: PRK06175 504832007664 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 504832007665 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 504832007666 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 504832007667 dimerization interface [polypeptide binding]; other site 504832007668 active site 504832007669 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 504832007670 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 504832007671 pyruvate phosphate dikinase; Provisional; Region: PRK09279 504832007672 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 504832007673 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 504832007674 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 504832007675 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 504832007676 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 504832007677 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 504832007678 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 504832007679 dimer interface [polypeptide binding]; other site 504832007680 motif 1; other site 504832007681 active site 504832007682 motif 2; other site 504832007683 motif 3; other site 504832007684 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 504832007685 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 504832007686 tandem repeat interface [polypeptide binding]; other site 504832007687 oligomer interface [polypeptide binding]; other site 504832007688 active site residues [active] 504832007689 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 504832007690 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 504832007691 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 504832007692 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 504832007693 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 504832007694 substrate binding pocket [chemical binding]; other site 504832007695 chain length determination region; other site 504832007696 substrate-Mg2+ binding site; other site 504832007697 catalytic residues [active] 504832007698 aspartate-rich region 1; other site 504832007699 active site lid residues [active] 504832007700 aspartate-rich region 2; other site 504832007701 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 504832007702 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 504832007703 TPR motif; other site 504832007704 binding surface 504832007705 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 504832007706 binding surface 504832007707 TPR motif; other site 504832007708 TPR repeat; Region: TPR_11; pfam13414 504832007709 TPR repeat; Region: TPR_11; pfam13414 504832007710 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 504832007711 binding surface 504832007712 TPR motif; other site 504832007713 Tetratricopeptide repeat; Region: TPR_16; pfam13432 504832007714 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 504832007715 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 504832007716 hydroxyglutarate oxidase; Provisional; Region: PRK11728 504832007717 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 504832007718 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 504832007719 Fe-S cluster binding site [ion binding]; other site 504832007720 active site 504832007721 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 504832007722 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832007723 NAD(P) binding site [chemical binding]; other site 504832007724 active site 504832007725 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 504832007726 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832007727 putative substrate translocation pore; other site 504832007728 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832007729 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832007730 DNA-binding site [nucleotide binding]; DNA binding site 504832007731 FCD domain; Region: FCD; pfam07729 504832007732 oxalate/formate antiporter; Region: oxa_formateAnti; TIGR04259 504832007733 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 504832007734 putative substrate translocation pore; other site 504832007735 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 504832007736 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 504832007737 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 504832007738 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 504832007739 RNA/DNA hybrid binding site [nucleotide binding]; other site 504832007740 active site 504832007741 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 504832007742 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 504832007743 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 504832007744 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 504832007745 FeS/SAM binding site; other site 504832007746 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 504832007747 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 504832007748 MPT binding site; other site 504832007749 trimer interface [polypeptide binding]; other site 504832007750 Predicted metalloprotease [General function prediction only]; Region: COG2321 504832007751 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 504832007752 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 504832007753 DNA methylase; Region: N6_N4_Mtase; pfam01555 504832007754 glutathionine S-transferase; Provisional; Region: PRK10542 504832007755 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 504832007756 C-terminal domain interface [polypeptide binding]; other site 504832007757 GSH binding site (G-site) [chemical binding]; other site 504832007758 dimer interface [polypeptide binding]; other site 504832007759 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 504832007760 dimer interface [polypeptide binding]; other site 504832007761 N-terminal domain interface [polypeptide binding]; other site 504832007762 substrate binding pocket (H-site) [chemical binding]; other site 504832007763 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 504832007764 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 504832007765 minor groove reading motif; other site 504832007766 helix-hairpin-helix signature motif; other site 504832007767 substrate binding pocket [chemical binding]; other site 504832007768 active site 504832007769 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 504832007770 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 504832007771 DNA binding and oxoG recognition site [nucleotide binding] 504832007772 Protein of unknown function (DUF721); Region: DUF721; cl02324 504832007773 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 504832007774 Thioredoxin; Region: Thioredoxin_4; pfam13462 504832007775 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 504832007776 AAA domain; Region: AAA_23; pfam13476 504832007777 Walker A/P-loop; other site 504832007778 ATP binding site [chemical binding]; other site 504832007779 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 504832007780 ABC transporter signature motif; other site 504832007781 Walker B; other site 504832007782 D-loop; other site 504832007783 H-loop/switch region; other site 504832007784 Mitochondrial small ribosomal subunit Rsm22; Region: Rsm22; cl17847 504832007785 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 504832007786 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 504832007787 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 504832007788 Peptidase family M48; Region: Peptidase_M48; cl12018 504832007789 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 504832007790 AAA domain; Region: AAA_31; pfam13614 504832007791 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832007792 active site 504832007793 anthranilate synthase; Provisional; Region: PRK13566 504832007794 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 504832007795 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 504832007796 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 504832007797 glutamine binding [chemical binding]; other site 504832007798 catalytic triad [active] 504832007799 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 504832007800 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 504832007801 cytochrome b; Provisional; Region: CYTB; MTH00156 504832007802 Qi binding site; other site 504832007803 intrachain domain interface; other site 504832007804 interchain domain interface [polypeptide binding]; other site 504832007805 heme bH binding site [chemical binding]; other site 504832007806 heme bL binding site [chemical binding]; other site 504832007807 Qo binding site; other site 504832007808 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 504832007809 interchain domain interface [polypeptide binding]; other site 504832007810 intrachain domain interface; other site 504832007811 Qi binding site; other site 504832007812 Qo binding site; other site 504832007813 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 504832007814 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 504832007815 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 504832007816 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 504832007817 [2Fe-2S] cluster binding site [ion binding]; other site 504832007818 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 504832007819 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 504832007820 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 504832007821 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 504832007822 active site 504832007823 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 504832007824 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl17752 504832007825 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832007826 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 504832007827 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 504832007828 active site 504832007829 NTP binding site [chemical binding]; other site 504832007830 metal binding triad [ion binding]; metal-binding site 504832007831 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 504832007832 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 504832007833 putative active site [active] 504832007834 putative CoA binding site [chemical binding]; other site 504832007835 nudix motif; other site 504832007836 metal binding site [ion binding]; metal-binding site 504832007837 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3816 504832007838 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 504832007839 MoxR-like ATPases [General function prediction only]; Region: COG0714 504832007840 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 504832007841 Walker A motif; other site 504832007842 ATP binding site [chemical binding]; other site 504832007843 Walker B motif; other site 504832007844 arginine finger; other site 504832007845 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 504832007846 Protein of unknown function DUF58; Region: DUF58; pfam01882 504832007847 N-terminal double-transmembrane domain; Region: two_anch; TIGR02226 504832007848 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 504832007849 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 504832007850 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 504832007851 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 504832007852 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 504832007853 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 504832007854 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 504832007855 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 504832007856 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 504832007857 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832007858 Coenzyme A binding pocket [chemical binding]; other site 504832007859 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 504832007860 nudix motif; other site 504832007861 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 504832007862 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832007863 active site 504832007864 metal binding site [ion binding]; metal-binding site 504832007865 isocitrate lyase; Provisional; Region: PRK15063 504832007866 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 504832007867 tetramer interface [polypeptide binding]; other site 504832007868 active site 504832007869 Mg2+/Mn2+ binding site [ion binding]; other site 504832007870 isocitrate lyase; Region: PLN02892 504832007871 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 504832007872 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 504832007873 non-specific DNA binding site [nucleotide binding]; other site 504832007874 salt bridge; other site 504832007875 sequence-specific DNA binding site [nucleotide binding]; other site 504832007876 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 504832007877 Domain of unknown function (DUF955); Region: DUF955; pfam06114 504832007878 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 504832007879 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 504832007880 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 504832007881 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 504832007882 hydroxyglutarate oxidase; Provisional; Region: PRK11728 504832007883 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 504832007884 thiS-thiF/thiG interaction site; other site 504832007885 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 504832007886 ThiS interaction site; other site 504832007887 putative active site [active] 504832007888 tetramer interface [polypeptide binding]; other site 504832007889 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 504832007890 thiamine phosphate binding site [chemical binding]; other site 504832007891 active site 504832007892 pyrophosphate binding site [ion binding]; other site 504832007893 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 504832007894 ThiC-associated domain; Region: ThiC-associated; pfam13667 504832007895 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 504832007896 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 504832007897 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 504832007898 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 504832007899 hypothetical protein; Provisional; Region: PRK06489 504832007900 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 504832007901 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 504832007902 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 504832007903 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 504832007904 heme binding site [chemical binding]; other site 504832007905 ferroxidase pore; other site 504832007906 ferroxidase diiron center [ion binding]; other site 504832007907 lytic murein transglycosylase; Region: MltB_2; TIGR02283 504832007908 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 504832007909 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832007910 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 504832007911 hypothetical protein; Provisional; Region: PRK05208 504832007912 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 504832007913 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 504832007914 S-adenosylmethionine binding site [chemical binding]; other site 504832007915 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 504832007916 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832007917 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832007918 ABC transporter; Region: ABC_tran_2; pfam12848 504832007919 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832007920 glutamate dehydrogenase; Provisional; Region: PRK09414 504832007921 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 504832007922 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 504832007923 NAD(P) binding site [chemical binding]; other site 504832007924 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832007925 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832007926 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 504832007927 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 504832007928 active site residue [active] 504832007929 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 504832007930 active site residue [active] 504832007931 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 504832007932 active site 504832007933 catalytic residue [active] 504832007934 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 504832007935 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 504832007936 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 504832007937 Walker A motif; other site 504832007938 ATP binding site [chemical binding]; other site 504832007939 Walker B motif; other site 504832007940 arginine finger; other site 504832007941 Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Region: GIY-YIG_SLX1_like; cd10449 504832007942 GIY-YIG motif/motif A; other site 504832007943 putative active site [active] 504832007944 putative metal binding site [ion binding]; other site 504832007945 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 504832007946 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 504832007947 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 504832007948 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 504832007949 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 504832007950 active site 504832007951 homodimer interface [polypeptide binding]; other site 504832007952 catalytic site [active] 504832007953 acceptor binding site [chemical binding]; other site 504832007954 glycogen branching enzyme; Provisional; Region: PRK05402 504832007955 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 504832007956 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 504832007957 active site 504832007958 catalytic site [active] 504832007959 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 504832007960 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 504832007961 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 504832007962 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 504832007963 active site 504832007964 catalytic site [active] 504832007965 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 504832007966 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 504832007967 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 504832007968 catalytic site [active] 504832007969 active site 504832007970 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 504832007971 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 504832007972 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 504832007973 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 504832007974 active site 504832007975 catalytic site [active] 504832007976 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 504832007977 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 504832007978 tetramerization interface [polypeptide binding]; other site 504832007979 NAD(P) binding site [chemical binding]; other site 504832007980 catalytic residues [active] 504832007981 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 504832007982 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 504832007983 tetramer interface [polypeptide binding]; other site 504832007984 active site 504832007985 Mg2+/Mn2+ binding site [ion binding]; other site 504832007986 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 504832007987 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS)...; Region: Ec2MCS_like_1; cd06117 504832007988 dimer interface [polypeptide binding]; other site 504832007989 active site 504832007990 citrylCoA binding site [chemical binding]; other site 504832007991 oxalacetate/citrate binding site [chemical binding]; other site 504832007992 coenzyme A binding site [chemical binding]; other site 504832007993 catalytic triad [active] 504832007994 Uncharacterized protein involved in propionate catabolism [General function prediction only]; Region: PrpD; COG2079 504832007995 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 504832007996 Predicted permeases [General function prediction only]; Region: COG0679 504832007997 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 504832007998 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 504832007999 putative substrate translocation pore; other site 504832008000 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832008001 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 504832008002 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 504832008003 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832008004 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832008005 metal binding site [ion binding]; metal-binding site 504832008006 active site 504832008007 I-site; other site 504832008008 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 504832008009 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 504832008010 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 504832008011 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 504832008012 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 504832008013 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 504832008014 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832008015 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008016 active site 504832008017 phosphorylation site [posttranslational modification] 504832008018 intermolecular recognition site; other site 504832008019 dimerization interface [polypeptide binding]; other site 504832008020 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 504832008021 DNA binding site [nucleotide binding] 504832008022 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008023 active site 504832008024 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832008025 phosphorylation site [posttranslational modification] 504832008026 intermolecular recognition site; other site 504832008027 dimerization interface [polypeptide binding]; other site 504832008028 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 504832008029 dimer interface [polypeptide binding]; other site 504832008030 phosphorylation site [posttranslational modification] 504832008031 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 504832008032 ATP binding site [chemical binding]; other site 504832008033 G-X-G motif; other site 504832008034 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008035 active site 504832008036 phosphorylation site [posttranslational modification] 504832008037 intermolecular recognition site; other site 504832008038 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 504832008039 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832008040 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 504832008041 dimer interface [polypeptide binding]; other site 504832008042 phosphorylation site [posttranslational modification] 504832008043 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 504832008044 ATP binding site [chemical binding]; other site 504832008045 Mg2+ binding site [ion binding]; other site 504832008046 G-X-G motif; other site 504832008047 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 504832008048 TPP-binding site [chemical binding]; other site 504832008049 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 504832008050 dimer interface [polypeptide binding]; other site 504832008051 PYR/PP interface [polypeptide binding]; other site 504832008052 TPP binding site [chemical binding]; other site 504832008053 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 504832008054 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 504832008055 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 504832008056 NMT1/THI5 like; Region: NMT1; pfam09084 504832008057 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832008058 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 504832008059 dimer interface [polypeptide binding]; other site 504832008060 conserved gate region; other site 504832008061 putative PBP binding loops; other site 504832008062 ABC-ATPase subunit interface; other site 504832008063 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832008064 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832008065 Walker A/P-loop; other site 504832008066 ATP binding site [chemical binding]; other site 504832008067 Q-loop/lid; other site 504832008068 ABC transporter signature motif; other site 504832008069 Walker B; other site 504832008070 D-loop; other site 504832008071 H-loop/switch region; other site 504832008072 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 504832008073 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 504832008074 putative NAD(P) binding site [chemical binding]; other site 504832008075 putative active site [active] 504832008076 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832008077 DNA-binding site [nucleotide binding]; DNA binding site 504832008078 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832008079 FCD domain; Region: FCD; pfam07729 504832008080 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 504832008081 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 504832008082 heme-binding site [chemical binding]; other site 504832008083 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832008084 dimer interface [polypeptide binding]; other site 504832008085 putative CheW interface [polypeptide binding]; other site 504832008086 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 504832008087 FHIPEP family; Region: FHIPEP; pfam00771 504832008088 Anti-sigma-K factor rskA; Region: RskA; pfam10099 504832008089 RNA polymerase sigma factor; Provisional; Region: PRK12514 504832008090 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832008091 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 504832008092 DNA binding residues [nucleotide binding] 504832008093 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 504832008094 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 504832008095 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 504832008096 Walker A motif/ATP binding site; other site 504832008097 Walker B motif; other site 504832008098 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832008099 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008100 active site 504832008101 phosphorylation site [posttranslational modification] 504832008102 intermolecular recognition site; other site 504832008103 dimerization interface [polypeptide binding]; other site 504832008104 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 504832008105 DNA binding site [nucleotide binding] 504832008106 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 504832008107 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 504832008108 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 504832008109 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 504832008110 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008111 active site 504832008112 phosphorylation site [posttranslational modification] 504832008113 intermolecular recognition site; other site 504832008114 dimerization interface [polypeptide binding]; other site 504832008115 CheB methylesterase; Region: CheB_methylest; pfam01339 504832008116 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008117 Response regulator receiver domain; Region: Response_reg; pfam00072 504832008118 active site 504832008119 phosphorylation site [posttranslational modification] 504832008120 intermolecular recognition site; other site 504832008121 dimerization interface [polypeptide binding]; other site 504832008122 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 504832008123 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 504832008124 putative binding surface; other site 504832008125 active site 504832008126 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 504832008127 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 504832008128 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 504832008129 ATP binding site [chemical binding]; other site 504832008130 Mg2+ binding site [ion binding]; other site 504832008131 G-X-G motif; other site 504832008132 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 504832008133 Response regulator receiver domain; Region: Response_reg; pfam00072 504832008134 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008135 active site 504832008136 phosphorylation site [posttranslational modification] 504832008137 intermolecular recognition site; other site 504832008138 dimerization interface [polypeptide binding]; other site 504832008139 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 504832008140 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 504832008141 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 504832008142 active site 504832008143 Protein of unknown function (DUF1134); Region: DUF1134; pfam06577 504832008144 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 504832008145 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832008146 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832008147 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 504832008148 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 504832008149 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 504832008150 putative active site [active] 504832008151 heme pocket [chemical binding]; other site 504832008152 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 504832008153 putative active site [active] 504832008154 heme pocket [chemical binding]; other site 504832008155 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 504832008156 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 504832008157 dimer interface [polypeptide binding]; other site 504832008158 putative CheW interface [polypeptide binding]; other site 504832008159 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 504832008160 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 504832008161 substrate binding site [chemical binding]; other site 504832008162 active site 504832008163 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 504832008164 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 504832008165 domain interfaces; other site 504832008166 active site 504832008167 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 504832008168 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 504832008169 Ferredoxin [Energy production and conversion]; Region: COG1146 504832008170 4Fe-4S binding domain; Region: Fer4; pfam00037 504832008171 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 504832008172 PAS domain S-box; Region: sensory_box; TIGR00229 504832008173 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 504832008174 putative active site [active] 504832008175 heme pocket [chemical binding]; other site 504832008176 PAS domain S-box; Region: sensory_box; TIGR00229 504832008177 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 504832008178 putative active site [active] 504832008179 heme pocket [chemical binding]; other site 504832008180 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 504832008181 dimer interface [polypeptide binding]; other site 504832008182 phosphorylation site [posttranslational modification] 504832008183 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 504832008184 ATP binding site [chemical binding]; other site 504832008185 Mg2+ binding site [ion binding]; other site 504832008186 G-X-G motif; other site 504832008187 response regulator FixJ; Provisional; Region: fixJ; PRK09390 504832008188 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008189 active site 504832008190 phosphorylation site [posttranslational modification] 504832008191 intermolecular recognition site; other site 504832008192 dimerization interface [polypeptide binding]; other site 504832008193 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 504832008194 DNA binding residues [nucleotide binding] 504832008195 dimerization interface [polypeptide binding]; other site 504832008196 Response regulator receiver domain; Region: Response_reg; pfam00072 504832008197 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008198 active site 504832008199 phosphorylation site [posttranslational modification] 504832008200 intermolecular recognition site; other site 504832008201 dimerization interface [polypeptide binding]; other site 504832008202 transcriptional regulator FixK; Provisional; Region: fixK; PRK09391 504832008203 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 504832008204 ligand binding site [chemical binding]; other site 504832008205 flexible hinge region; other site 504832008206 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 504832008207 putative switch regulator; other site 504832008208 non-specific DNA interactions [nucleotide binding]; other site 504832008209 DNA binding site [nucleotide binding] 504832008210 sequence specific DNA binding site [nucleotide binding]; other site 504832008211 putative cAMP binding site [chemical binding]; other site 504832008212 NnrS protein; Region: NnrS; pfam05940 504832008213 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 504832008214 Low-spin heme binding site [chemical binding]; other site 504832008215 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 504832008216 Putative water exit pathway; other site 504832008217 Binuclear center (active site) [active] 504832008218 Putative proton exit pathway; other site 504832008219 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 504832008220 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 504832008221 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 504832008222 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 504832008223 Cytochrome c; Region: Cytochrom_C; pfam00034 504832008224 Cytochrome c; Region: Cytochrom_C; pfam00034 504832008225 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 504832008226 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832008227 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 504832008228 metal-binding site [ion binding] 504832008229 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832008230 Soluble P-type ATPase [General function prediction only]; Region: COG4087 504832008231 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 504832008232 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 504832008233 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 504832008234 RNA binding surface [nucleotide binding]; other site 504832008235 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 504832008236 active site 504832008237 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 504832008238 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 504832008239 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832008240 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 504832008241 DNA binding residues [nucleotide binding] 504832008242 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 504832008243 active site 504832008244 substrate binding site [chemical binding]; other site 504832008245 cosubstrate binding site; other site 504832008246 catalytic site [active] 504832008247 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 504832008248 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 504832008249 GDP-binding site [chemical binding]; other site 504832008250 ACT binding site; other site 504832008251 IMP binding site; other site 504832008252 EamA-like transporter family; Region: EamA; pfam00892 504832008253 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 504832008254 EamA-like transporter family; Region: EamA; pfam00892 504832008255 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 504832008256 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 504832008257 ligand binding site [chemical binding]; other site 504832008258 NAD binding site [chemical binding]; other site 504832008259 dimerization interface [polypeptide binding]; other site 504832008260 catalytic site [active] 504832008261 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 504832008262 putative L-serine binding site [chemical binding]; other site 504832008263 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 504832008264 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832008265 catalytic residue [active] 504832008266 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 504832008267 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832008268 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832008269 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 504832008270 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832008271 putative substrate translocation pore; other site 504832008272 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 504832008273 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 504832008274 active site 504832008275 substrate binding site [chemical binding]; other site 504832008276 metal binding site [ion binding]; metal-binding site 504832008277 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 504832008278 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 504832008279 phosphate binding site [ion binding]; other site 504832008280 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 504832008281 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 504832008282 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 504832008283 shikimate binding site; other site 504832008284 NAD(P) binding site [chemical binding]; other site 504832008285 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 504832008286 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 504832008287 Sulfate transporter family; Region: Sulfate_transp; pfam00916 504832008288 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 504832008289 Protein of unknown function (DUF992); Region: DUF992; pfam06186 504832008290 Protein of unknown function (DUF992); Region: DUF992; pfam06186 504832008291 aspartate aminotransferase; Provisional; Region: PRK05764 504832008292 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 504832008293 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832008294 homodimer interface [polypeptide binding]; other site 504832008295 catalytic residue [active] 504832008296 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 504832008297 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832008298 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 504832008299 putative C-terminal domain interface [polypeptide binding]; other site 504832008300 putative GSH binding site (G-site) [chemical binding]; other site 504832008301 putative dimer interface [polypeptide binding]; other site 504832008302 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 504832008303 N-terminal domain interface [polypeptide binding]; other site 504832008304 dimer interface [polypeptide binding]; other site 504832008305 substrate binding pocket (H-site) [chemical binding]; other site 504832008306 Protein of unknown function, DUF486; Region: DUF486; cl01236 504832008307 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 504832008308 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 504832008309 putative acyl-acceptor binding pocket; other site 504832008310 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 504832008311 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 504832008312 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 504832008313 putative C-terminal domain interface [polypeptide binding]; other site 504832008314 putative GSH binding site (G-site) [chemical binding]; other site 504832008315 putative dimer interface [polypeptide binding]; other site 504832008316 C-terminal, alpha helical domain of Beta etherase LigE; Region: GST_C_etherase_LigE; cd03202 504832008317 putative N-terminal domain interface [polypeptide binding]; other site 504832008318 putative dimer interface [polypeptide binding]; other site 504832008319 putative substrate binding pocket (H-site) [chemical binding]; other site 504832008320 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 504832008321 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 504832008322 C-terminal domain interface [polypeptide binding]; other site 504832008323 GSH binding site (G-site) [chemical binding]; other site 504832008324 dimer interface [polypeptide binding]; other site 504832008325 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 504832008326 N-terminal domain interface [polypeptide binding]; other site 504832008327 putative dimer interface [polypeptide binding]; other site 504832008328 active site 504832008329 excinuclease ABC subunit B; Provisional; Region: PRK05298 504832008330 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 504832008331 ATP binding site [chemical binding]; other site 504832008332 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 504832008333 nucleotide binding region [chemical binding]; other site 504832008334 ATP-binding site [chemical binding]; other site 504832008335 Ultra-violet resistance protein B; Region: UvrB; pfam12344 504832008336 UvrB/uvrC motif; Region: UVR; pfam02151 504832008337 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 504832008338 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832008339 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832008340 Walker A/P-loop; other site 504832008341 ATP binding site [chemical binding]; other site 504832008342 Q-loop/lid; other site 504832008343 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832008344 ABC transporter signature motif; other site 504832008345 Walker B; other site 504832008346 D-loop; other site 504832008347 ABC transporter; Region: ABC_tran_2; pfam12848 504832008348 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 504832008349 Domain of unknown function (DUF4282); Region: DUF4282; pfam14110 504832008350 GTP-binding protein YchF; Reviewed; Region: PRK09601 504832008351 YchF GTPase; Region: YchF; cd01900 504832008352 G1 box; other site 504832008353 GTP/Mg2+ binding site [chemical binding]; other site 504832008354 Switch I region; other site 504832008355 G2 box; other site 504832008356 Switch II region; other site 504832008357 G3 box; other site 504832008358 G4 box; other site 504832008359 G5 box; other site 504832008360 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 504832008361 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 504832008362 putative active site [active] 504832008363 catalytic residue [active] 504832008364 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 504832008365 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 504832008366 5S rRNA interface [nucleotide binding]; other site 504832008367 CTC domain interface [polypeptide binding]; other site 504832008368 L16 interface [polypeptide binding]; other site 504832008369 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 504832008370 Zn2+ binding site [ion binding]; other site 504832008371 Mg2+ binding site [ion binding]; other site 504832008372 Membrane fusogenic activity; Region: BMFP; pfam04380 504832008373 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 504832008374 Uncharacterized conserved protein [Function unknown]; Region: COG1565 504832008375 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 504832008376 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 504832008377 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 504832008378 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 504832008379 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832008380 active site 504832008381 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 504832008382 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 504832008383 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 504832008384 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832008385 HAMP domain; Region: HAMP; pfam00672 504832008386 dimerization interface [polypeptide binding]; other site 504832008387 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 504832008388 dimer interface [polypeptide binding]; other site 504832008389 phosphorylation site [posttranslational modification] 504832008390 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 504832008391 ATP binding site [chemical binding]; other site 504832008392 Mg2+ binding site [ion binding]; other site 504832008393 G-X-G motif; other site 504832008394 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008395 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832008396 active site 504832008397 phosphorylation site [posttranslational modification] 504832008398 intermolecular recognition site; other site 504832008399 dimerization interface [polypeptide binding]; other site 504832008400 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 504832008401 DNA binding site [nucleotide binding] 504832008402 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 504832008403 MarR family; Region: MarR_2; pfam12802 504832008404 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 504832008405 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 504832008406 homodimer interface [polypeptide binding]; other site 504832008407 substrate-cofactor binding pocket; other site 504832008408 catalytic residue [active] 504832008409 multidrug efflux protein; Reviewed; Region: PRK01766 504832008410 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 504832008411 cation binding site [ion binding]; other site 504832008412 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 504832008413 nucleoside/Zn binding site; other site 504832008414 dimer interface [polypeptide binding]; other site 504832008415 catalytic motif [active] 504832008416 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 504832008417 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 504832008418 S-adenosylmethionine binding site [chemical binding]; other site 504832008419 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 504832008420 MoaE homodimer interface [polypeptide binding]; other site 504832008421 MoaD interaction [polypeptide binding]; other site 504832008422 active site residues [active] 504832008423 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 504832008424 MoaE interaction surface [polypeptide binding]; other site 504832008425 MoeB interaction surface [polypeptide binding]; other site 504832008426 thiocarboxylated glycine; other site 504832008427 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 504832008428 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 504832008429 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 504832008430 GIY-YIG motif/motif A; other site 504832008431 active site 504832008432 catalytic site [active] 504832008433 putative DNA binding site [nucleotide binding]; other site 504832008434 metal binding site [ion binding]; metal-binding site 504832008435 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 504832008436 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832008437 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 504832008438 DNA-binding site [nucleotide binding]; DNA binding site 504832008439 RNA-binding motif; other site 504832008440 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 504832008441 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 504832008442 B1 nucleotide binding pocket [chemical binding]; other site 504832008443 B2 nucleotide binding pocket [chemical binding]; other site 504832008444 CAS motifs; other site 504832008445 active site 504832008446 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 504832008447 active site 1 [active] 504832008448 dimer interface [polypeptide binding]; other site 504832008449 hexamer interface [polypeptide binding]; other site 504832008450 active site 2 [active] 504832008451 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 504832008452 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 504832008453 dimer interface [polypeptide binding]; other site 504832008454 motif 1; other site 504832008455 motif 2; other site 504832008456 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 504832008457 active site 504832008458 motif 3; other site 504832008459 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 504832008460 anticodon binding site; other site 504832008461 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 504832008462 putative active site [active] 504832008463 Predicted membrane protein [Function unknown]; Region: COG4655 504832008464 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 504832008465 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 504832008466 TadE-like protein; Region: TadE; pfam07811 504832008467 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 504832008468 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 504832008469 inhibitor-cofactor binding pocket; inhibition site 504832008470 pyridoxal 5'-phosphate binding site [chemical binding]; other site 504832008471 catalytic residue [active] 504832008472 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 504832008473 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 504832008474 Haloacid Dehalogenase Superfamily Class (subfamily) IIA; Region: HAD-SF-IIA; TIGR01460 504832008475 active site 504832008476 motif I; other site 504832008477 motif II; other site 504832008478 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 504832008479 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 504832008480 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 504832008481 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008482 active site 504832008483 phosphorylation site [posttranslational modification] 504832008484 intermolecular recognition site; other site 504832008485 dimerization interface [polypeptide binding]; other site 504832008486 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 504832008487 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 504832008488 active site 504832008489 Riboflavin kinase; Region: Flavokinase; smart00904 504832008490 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 504832008491 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 504832008492 active site 504832008493 HIGH motif; other site 504832008494 nucleotide binding site [chemical binding]; other site 504832008495 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 504832008496 active site 504832008497 KMSKS motif; other site 504832008498 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 504832008499 tRNA binding surface [nucleotide binding]; other site 504832008500 anticodon binding site; other site 504832008501 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 504832008502 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 504832008503 N-terminal plug; other site 504832008504 ligand-binding site [chemical binding]; other site 504832008505 lipoprotein signal peptidase; Provisional; Region: PRK14796 504832008506 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 504832008507 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 504832008508 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 504832008509 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 504832008510 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 504832008511 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 504832008512 hypothetical protein; Provisional; Region: PRK09256 504832008513 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 504832008514 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 504832008515 ATP binding site [chemical binding]; other site 504832008516 Mg2+ binding site [ion binding]; other site 504832008517 G-X-G motif; other site 504832008518 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 504832008519 ATP binding site [chemical binding]; other site 504832008520 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 504832008521 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 504832008522 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 504832008523 S-adenosylmethionine binding site [chemical binding]; other site 504832008524 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 504832008525 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 504832008526 RNA binding surface [nucleotide binding]; other site 504832008527 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 504832008528 active site 504832008529 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 504832008530 nucleoside/Zn binding site; other site 504832008531 dimer interface [polypeptide binding]; other site 504832008532 catalytic motif [active] 504832008533 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832008534 Coenzyme A binding pocket [chemical binding]; other site 504832008535 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 504832008536 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 504832008537 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 504832008538 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 504832008539 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 504832008540 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 504832008541 generic binding surface II; other site 504832008542 generic binding surface I; other site 504832008543 Cytochrome c2 [Energy production and conversion]; Region: COG3474 504832008544 rusticyanin; Region: rusti_cyanin; TIGR03095 504832008545 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 504832008546 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832008547 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3908 504832008548 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 504832008549 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 504832008550 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 504832008551 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 504832008552 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 504832008553 putative acyl-acceptor binding pocket; other site 504832008554 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 504832008555 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 504832008556 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 504832008557 active site 504832008558 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 504832008559 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12878 504832008560 UbiA prenyltransferase family; Region: UbiA; pfam01040 504832008561 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 504832008562 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 504832008563 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 504832008564 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 504832008565 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 504832008566 motif 1; other site 504832008567 dimer interface [polypeptide binding]; other site 504832008568 active site 504832008569 motif 2; other site 504832008570 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 504832008571 active site 504832008572 motif 3; other site 504832008573 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 504832008574 ATP phosphoribosyltransferase catalytic subunit; Provisional; Region: hisG; PRK13583 504832008575 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 504832008576 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 504832008577 Ligand binding site; other site 504832008578 Putative Catalytic site; other site 504832008579 DXD motif; other site 504832008580 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 504832008581 putative active site [active] 504832008582 YdjC motif; other site 504832008583 Mg binding site [ion binding]; other site 504832008584 putative homodimer interface [polypeptide binding]; other site 504832008585 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 504832008586 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832008587 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832008588 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 504832008589 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 504832008590 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832008591 putative substrate translocation pore; other site 504832008592 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 504832008593 oligomerisation interface [polypeptide binding]; other site 504832008594 mobile loop; other site 504832008595 roof hairpin; other site 504832008596 chaperonin GroEL; Reviewed; Region: groEL; PRK12852 504832008597 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 504832008598 ring oligomerisation interface [polypeptide binding]; other site 504832008599 ATP/Mg binding site [chemical binding]; other site 504832008600 stacking interactions; other site 504832008601 hinge regions; other site 504832008602 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 504832008603 L-lactate permease; Region: Lactate_perm; cl00701 504832008604 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 504832008605 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 504832008606 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 504832008607 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 504832008608 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 504832008609 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 504832008610 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 504832008611 Cysteine-rich domain; Region: CCG; pfam02754 504832008612 Cysteine-rich domain; Region: CCG; pfam02754 504832008613 FAD binding domain; Region: FAD_binding_4; pfam01565 504832008614 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 504832008615 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 504832008616 FAD binding domain; Region: FAD_binding_4; pfam01565 504832008617 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 504832008618 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832008619 putative substrate translocation pore; other site 504832008620 FtsH Extracellular; Region: FtsH_ext; pfam06480 504832008621 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 504832008622 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 504832008623 Walker A motif; other site 504832008624 ATP binding site [chemical binding]; other site 504832008625 Walker B motif; other site 504832008626 arginine finger; other site 504832008627 Peptidase family M41; Region: Peptidase_M41; pfam01434 504832008628 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 504832008629 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 504832008630 Ligand Binding Site [chemical binding]; other site 504832008631 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 504832008632 Tetratricopeptide repeat; Region: TPR_6; pfam13174 504832008633 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 504832008634 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 504832008635 ligand binding site [chemical binding]; other site 504832008636 translocation protein TolB; Provisional; Region: tolB; PRK05137 504832008637 TolB amino-terminal domain; Region: TolB_N; pfam04052 504832008638 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 504832008639 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 504832008640 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 504832008641 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 504832008642 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 504832008643 TolR protein; Region: tolR; TIGR02801 504832008644 TolQ protein; Region: tolQ; TIGR02796 504832008645 Protein of unknown function (DUF2852); Region: DUF2852; pfam11014 504832008646 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 504832008647 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 504832008648 WHG domain; Region: WHG; pfam13305 504832008649 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 504832008650 active site 504832008651 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 504832008652 nudix motif; other site 504832008653 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 504832008654 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 504832008655 Walker A motif; other site 504832008656 ATP binding site [chemical binding]; other site 504832008657 Walker B motif; other site 504832008658 arginine finger; other site 504832008659 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 504832008660 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 504832008661 RuvA N terminal domain; Region: RuvA_N; pfam01330 504832008662 Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase; cl00205 504832008663 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 504832008664 active site 504832008665 putative DNA-binding cleft [nucleotide binding]; other site 504832008666 dimer interface [polypeptide binding]; other site 504832008667 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 504832008668 MgtE intracellular N domain; Region: MgtE_N; pfam03448 504832008669 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 504832008670 Divalent cation transporter; Region: MgtE; pfam01769 504832008671 hypothetical protein; Validated; Region: PRK00110 504832008672 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 504832008673 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 504832008674 putative active site [active] 504832008675 metal binding site [ion binding]; metal-binding site 504832008676 homodimer binding site [polypeptide binding]; other site 504832008677 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 504832008678 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 504832008679 Cell division protein ZapA; Region: ZapA; pfam05164 504832008680 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 504832008681 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 504832008682 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 504832008683 TPP-binding site [chemical binding]; other site 504832008684 dimer interface [polypeptide binding]; other site 504832008685 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 504832008686 PYR/PP interface [polypeptide binding]; other site 504832008687 dimer interface [polypeptide binding]; other site 504832008688 TPP binding site [chemical binding]; other site 504832008689 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 504832008690 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 504832008691 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 504832008692 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 504832008693 Phosphoglycerate kinase; Region: PGK; pfam00162 504832008694 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 504832008695 substrate binding site [chemical binding]; other site 504832008696 hinge regions; other site 504832008697 ADP binding site [chemical binding]; other site 504832008698 catalytic site [active] 504832008699 Fructose-1,6-bisphosphate aldolase; Region: FBP_aldolase_I_a; cd00948 504832008700 active site 504832008701 intersubunit interface [polypeptide binding]; other site 504832008702 catalytic residue [active] 504832008703 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 504832008704 thiamine phosphate binding site [chemical binding]; other site 504832008705 active site 504832008706 pyrophosphate binding site [ion binding]; other site 504832008707 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 504832008708 Sel1-like repeats; Region: SEL1; smart00671 504832008709 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 504832008710 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 504832008711 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 504832008712 active site 504832008713 dimerization interface [polypeptide binding]; other site 504832008714 hypothetical protein; Validated; Region: PRK09039 504832008715 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 504832008716 ligand binding site [chemical binding]; other site 504832008717 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 504832008718 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832008719 Coenzyme A binding pocket [chemical binding]; other site 504832008720 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 504832008721 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832008722 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832008723 Walker A/P-loop; other site 504832008724 ATP binding site [chemical binding]; other site 504832008725 Q-loop/lid; other site 504832008726 ABC transporter signature motif; other site 504832008727 Walker B; other site 504832008728 D-loop; other site 504832008729 H-loop/switch region; other site 504832008730 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 504832008731 Protein of unknown function (DUF1465); Region: DUF1465; pfam07323 504832008732 Protein of unknown function (DUF1192); Region: DUF1192; pfam06698 504832008733 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 504832008734 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 504832008735 NAD(P) binding site [chemical binding]; other site 504832008736 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 504832008737 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 504832008738 PAS fold; Region: PAS_3; pfam08447 504832008739 putative active site [active] 504832008740 heme pocket [chemical binding]; other site 504832008741 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832008742 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832008743 metal binding site [ion binding]; metal-binding site 504832008744 active site 504832008745 I-site; other site 504832008746 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 504832008747 hypothetical protein; Validated; Region: PRK00228 504832008748 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 504832008749 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 504832008750 catalytic triad [active] 504832008751 dimer interface [polypeptide binding]; other site 504832008752 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 504832008753 RNA/DNA hybrid binding site [nucleotide binding]; other site 504832008754 active site 504832008755 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 504832008756 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 504832008757 putative active site [active] 504832008758 putative substrate binding site [chemical binding]; other site 504832008759 ATP binding site [chemical binding]; other site 504832008760 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 504832008761 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 504832008762 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 504832008763 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 504832008764 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 504832008765 catalytic residues [active] 504832008766 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 504832008767 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 504832008768 acyl-activating enzyme (AAE) consensus motif; other site 504832008769 putative AMP binding site [chemical binding]; other site 504832008770 putative active site [active] 504832008771 putative CoA binding site [chemical binding]; other site 504832008772 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 504832008773 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 504832008774 DctM-like transporters; Region: DctM; pfam06808 504832008775 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 504832008776 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 504832008777 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 504832008778 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 504832008779 Low-spin heme binding site [chemical binding]; other site 504832008780 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 504832008781 Putative water exit pathway; other site 504832008782 Binuclear center (active site) [active] 504832008783 Putative proton exit pathway; other site 504832008784 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 504832008785 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 504832008786 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 504832008787 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 504832008788 Cytochrome c; Region: Cytochrom_C; pfam00034 504832008789 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 504832008790 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 504832008791 4Fe-4S binding domain; Region: Fer4_5; pfam12801 504832008792 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 504832008793 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 504832008794 FixH; Region: FixH; pfam05751 504832008795 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 504832008796 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832008797 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832008798 DNA-binding site [nucleotide binding]; DNA binding site 504832008799 FCD domain; Region: FCD; pfam07729 504832008800 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 504832008801 CoA binding domain; Region: CoA_binding_2; pfam13380 504832008802 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 504832008803 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 504832008804 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 504832008805 NAD(P) binding site [chemical binding]; other site 504832008806 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 504832008807 Coenzyme A transferase; Region: CoA_trans; cl17247 504832008808 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 504832008809 Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like; Region: M20_ArgE_DapE_like; cd08659 504832008810 metal binding site [ion binding]; metal-binding site 504832008811 dimer interface [polypeptide binding]; other site 504832008812 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 504832008813 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; cd00640 504832008814 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 504832008815 catalytic residue [active] 504832008816 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 504832008817 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 504832008818 hypothetical protein; Provisional; Region: PRK05463 504832008819 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 504832008820 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 504832008821 dimer interface [polypeptide binding]; other site 504832008822 conserved gate region; other site 504832008823 putative PBP binding loops; other site 504832008824 ABC-ATPase subunit interface; other site 504832008825 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 504832008826 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 504832008827 Walker A/P-loop; other site 504832008828 ATP binding site [chemical binding]; other site 504832008829 Q-loop/lid; other site 504832008830 ABC transporter signature motif; other site 504832008831 Walker B; other site 504832008832 D-loop; other site 504832008833 H-loop/switch region; other site 504832008834 NMT1/THI5 like; Region: NMT1; pfam09084 504832008835 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 504832008836 membrane-bound complex binding site; other site 504832008837 hinge residues; other site 504832008838 Transcriptional regulators [Transcription]; Region: GntR; COG1802 504832008839 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832008840 DNA-binding site [nucleotide binding]; DNA binding site 504832008841 FCD domain; Region: FCD; pfam07729 504832008842 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 504832008843 NMT1/THI5 like; Region: NMT1; pfam09084 504832008844 Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A [Nucleotide transport and metabolism]; Region: XdhA; COG4630 504832008845 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 504832008846 FAD binding domain; Region: FAD_binding_4; pfam01565 504832008847 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 504832008848 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 504832008849 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 504832008850 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 504832008851 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 504832008852 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 504832008853 XdhC Rossmann domain; Region: XdhC_C; pfam13478 504832008854 Protein of unknown function (DUF3551); Region: DUF3551; pfam12071 504832008855 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832008856 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832008857 metal binding site [ion binding]; metal-binding site 504832008858 active site 504832008859 I-site; other site 504832008860 Predicted membrane protein [Function unknown]; Region: COG1238 504832008861 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 504832008862 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 504832008863 metal binding site [ion binding]; metal-binding site 504832008864 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 504832008865 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 504832008866 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832008867 Walker A/P-loop; other site 504832008868 ATP binding site [chemical binding]; other site 504832008869 Q-loop/lid; other site 504832008870 ABC transporter signature motif; other site 504832008871 Walker B; other site 504832008872 D-loop; other site 504832008873 H-loop/switch region; other site 504832008874 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 504832008875 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 504832008876 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 504832008877 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 504832008878 acyl-activating enzyme (AAE) consensus motif; other site 504832008879 putative AMP binding site [chemical binding]; other site 504832008880 putative active site [active] 504832008881 putative CoA binding site [chemical binding]; other site 504832008882 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 504832008883 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 504832008884 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 504832008885 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 504832008886 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 504832008887 NAD(P) binding site [chemical binding]; other site 504832008888 active site 504832008889 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 504832008890 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 504832008891 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 504832008892 Walker A/P-loop; other site 504832008893 ATP binding site [chemical binding]; other site 504832008894 Q-loop/lid; other site 504832008895 ABC transporter signature motif; other site 504832008896 Walker B; other site 504832008897 D-loop; other site 504832008898 H-loop/switch region; other site 504832008899 TOBE-like domain; Region: TOBE_3; pfam12857 504832008900 sulfate transport protein; Provisional; Region: cysT; CHL00187 504832008901 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 504832008902 dimer interface [polypeptide binding]; other site 504832008903 conserved gate region; other site 504832008904 putative PBP binding loops; other site 504832008905 ABC-ATPase subunit interface; other site 504832008906 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 504832008907 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 504832008908 dimer interface [polypeptide binding]; other site 504832008909 conserved gate region; other site 504832008910 putative PBP binding loops; other site 504832008911 ABC-ATPase subunit interface; other site 504832008912 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 504832008913 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 504832008914 substrate binding pocket [chemical binding]; other site 504832008915 membrane-bound complex binding site; other site 504832008916 hinge residues; other site 504832008917 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 504832008918 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 504832008919 Active Sites [active] 504832008920 siroheme synthase; Provisional; Region: cysG; PRK10637 504832008921 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 504832008922 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 504832008923 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 504832008924 active site 504832008925 SAM binding site [chemical binding]; other site 504832008926 homodimer interface [polypeptide binding]; other site 504832008927 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 504832008928 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 504832008929 catalytic loop [active] 504832008930 iron binding site [ion binding]; other site 504832008931 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 504832008932 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 504832008933 Active Sites [active] 504832008934 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 504832008935 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 504832008936 G1 box; other site 504832008937 putative GEF interaction site [polypeptide binding]; other site 504832008938 GTP/Mg2+ binding site [chemical binding]; other site 504832008939 Switch I region; other site 504832008940 G2 box; other site 504832008941 CysD dimerization site [polypeptide binding]; other site 504832008942 G3 box; other site 504832008943 Switch II region; other site 504832008944 G4 box; other site 504832008945 G5 box; other site 504832008946 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 504832008947 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 504832008948 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 504832008949 ligand-binding site [chemical binding]; other site 504832008950 malate synthase G; Provisional; Region: PRK02999 504832008951 active site 504832008952 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 504832008953 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 504832008954 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 504832008955 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 504832008956 Domain of unknown function DUF20; Region: UPF0118; pfam01594 504832008957 two-component response regulator; Provisional; Region: PRK09191 504832008958 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832008959 active site 504832008960 phosphorylation site [posttranslational modification] 504832008961 intermolecular recognition site; other site 504832008962 dimerization interface [polypeptide binding]; other site 504832008963 RNA polymerase sigma factor; Provisional; Region: PRK12540 504832008964 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832008965 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 504832008966 DNA binding residues [nucleotide binding] 504832008967 CHASE domain; Region: CHASE; cl01369 504832008968 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 504832008969 HWE histidine kinase; Region: HWE_HK; pfam07536 504832008970 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 504832008971 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 504832008972 ATP binding site [chemical binding]; other site 504832008973 Mg++ binding site [ion binding]; other site 504832008974 motif III; other site 504832008975 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 504832008976 nucleotide binding region [chemical binding]; other site 504832008977 ATP-binding site [chemical binding]; other site 504832008978 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 504832008979 rRNA binding site [nucleotide binding]; other site 504832008980 predicted 30S ribosome binding site; other site 504832008981 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 504832008982 DNA-binding site [nucleotide binding]; DNA binding site 504832008983 RNA-binding motif; other site 504832008984 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 504832008985 TadE-like protein; Region: TadE; pfam07811 504832008986 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 504832008987 TadE-like protein; Region: TadE; pfam07811 504832008988 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 504832008989 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 504832008990 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 504832008991 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 504832008992 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 504832008993 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 504832008994 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 504832008995 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 504832008996 Type IV pili component [Cell motility and secretion]; Region: COG5461 504832008997 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 504832008998 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 504832008999 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 504832009000 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 504832009001 ATP binding site [chemical binding]; other site 504832009002 Walker A motif; other site 504832009003 hexamer interface [polypeptide binding]; other site 504832009004 Walker B motif; other site 504832009005 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 504832009006 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 504832009007 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 504832009008 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 504832009009 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 504832009010 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 504832009011 binding surface 504832009012 TPR motif; other site 504832009013 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 504832009014 binding surface 504832009015 TPR motif; other site 504832009016 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 504832009017 interface (dimer of trimers) [polypeptide binding]; other site 504832009018 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 504832009019 Substrate-binding/catalytic site; other site 504832009020 Zn-binding sites [ion binding]; other site 504832009021 Src Homology 3 domain superfamily; Region: SH3; cl17036 504832009022 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 504832009023 NlpC/P60 family; Region: NLPC_P60; pfam00877 504832009024 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 504832009025 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009026 Walker A/P-loop; other site 504832009027 ATP binding site [chemical binding]; other site 504832009028 Q-loop/lid; other site 504832009029 ABC transporter signature motif; other site 504832009030 Walker B; other site 504832009031 D-loop; other site 504832009032 H-loop/switch region; other site 504832009033 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832009034 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009035 Walker A/P-loop; other site 504832009036 ATP binding site [chemical binding]; other site 504832009037 Q-loop/lid; other site 504832009038 ABC transporter signature motif; other site 504832009039 Walker B; other site 504832009040 D-loop; other site 504832009041 H-loop/switch region; other site 504832009042 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832009043 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 504832009044 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 504832009045 ABC-ATPase subunit interface; other site 504832009046 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 504832009047 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 504832009048 dimer interface [polypeptide binding]; other site 504832009049 conserved gate region; other site 504832009050 putative PBP binding loops; other site 504832009051 ABC-ATPase subunit interface; other site 504832009052 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 504832009053 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 504832009054 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 504832009055 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 504832009056 Cytochrome c2 [Energy production and conversion]; Region: COG3474 504832009057 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 504832009058 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 504832009059 Ligand binding site; other site 504832009060 oligomer interface; other site 504832009061 prephenate dehydratase; Provisional; Region: PRK11899 504832009062 Prephenate dehydratase; Region: PDT; pfam00800 504832009063 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 504832009064 putative L-Phe binding site [chemical binding]; other site 504832009065 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 504832009066 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 504832009067 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 504832009068 FAD binding site [chemical binding]; other site 504832009069 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 504832009070 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 504832009071 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 504832009072 substrate binding pocket [chemical binding]; other site 504832009073 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 504832009074 B12 binding site [chemical binding]; other site 504832009075 cobalt ligand [ion binding]; other site 504832009076 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 504832009077 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 504832009078 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 504832009079 N- and C-terminal domain interface [polypeptide binding]; other site 504832009080 active site 504832009081 MgATP binding site [chemical binding]; other site 504832009082 catalytic site [active] 504832009083 metal binding site [ion binding]; metal-binding site 504832009084 glycerol binding site [chemical binding]; other site 504832009085 homotetramer interface [polypeptide binding]; other site 504832009086 homodimer interface [polypeptide binding]; other site 504832009087 FBP binding site [chemical binding]; other site 504832009088 protein IIAGlc interface [polypeptide binding]; other site 504832009089 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 504832009090 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 504832009091 dimer interface [polypeptide binding]; other site 504832009092 active site 504832009093 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 504832009094 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 504832009095 MOFRL family; Region: MOFRL; pfam05161 504832009096 integrase; Provisional; Region: PRK09692 504832009097 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 504832009098 active site 504832009099 Int/Topo IB signature motif; other site 504832009100 Helix-turn-helix domain; Region: HTH_17; pfam12728 504832009101 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 504832009102 DNA binding site [nucleotide binding] 504832009103 active site 504832009104 Int/Topo IB signature motif; other site 504832009105 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 504832009106 DNA binding site [nucleotide binding] 504832009107 active site 504832009108 Int/Topo IB signature motif; other site 504832009109 catalytic residues [active] 504832009110 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 504832009111 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 504832009112 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832009113 CCC1-related family of proteins; Region: CCC1_like; cl00278 504832009114 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 504832009115 EF-hand domain pair; Region: EF_hand_5; pfam13499 504832009116 Ca2+ binding site [ion binding]; other site 504832009117 Protein of unknown function, DUF488; Region: DUF488; pfam04343 504832009118 Protein of unknown function (DUF2945); Region: DUF2945; pfam11160 504832009119 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 504832009120 Repair protein; Region: Repair_PSII; pfam04536 504832009121 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 504832009122 Repair protein; Region: Repair_PSII; pfam04536 504832009123 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 504832009124 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 504832009125 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 504832009126 substrate binding site [chemical binding]; other site 504832009127 THF binding site; other site 504832009128 zinc-binding site [ion binding]; other site 504832009129 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 504832009130 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 504832009131 Walker A/P-loop; other site 504832009132 ATP binding site [chemical binding]; other site 504832009133 Q-loop/lid; other site 504832009134 ABC transporter signature motif; other site 504832009135 Walker B; other site 504832009136 D-loop; other site 504832009137 H-loop/switch region; other site 504832009138 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 504832009139 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 504832009140 dimer interface [polypeptide binding]; other site 504832009141 conserved gate region; other site 504832009142 putative PBP binding loops; other site 504832009143 ABC-ATPase subunit interface; other site 504832009144 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 504832009145 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 504832009146 substrate binding pocket [chemical binding]; other site 504832009147 membrane-bound complex binding site; other site 504832009148 hinge residues; other site 504832009149 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 504832009150 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 504832009151 putative amidase; Provisional; Region: PRK06169 504832009152 Amidase; Region: Amidase; pfam01425 504832009153 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 504832009154 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832009155 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832009156 Walker A/P-loop; other site 504832009157 ATP binding site [chemical binding]; other site 504832009158 Q-loop/lid; other site 504832009159 ABC transporter signature motif; other site 504832009160 Walker B; other site 504832009161 D-loop; other site 504832009162 H-loop/switch region; other site 504832009163 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832009164 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 504832009165 TM-ABC transporter signature motif; other site 504832009166 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832009167 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832009168 Walker A/P-loop; other site 504832009169 ATP binding site [chemical binding]; other site 504832009170 Q-loop/lid; other site 504832009171 ABC transporter signature motif; other site 504832009172 Walker B; other site 504832009173 D-loop; other site 504832009174 H-loop/switch region; other site 504832009175 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832009176 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 504832009177 TM-ABC transporter signature motif; other site 504832009178 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_2; cd06335 504832009179 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 504832009180 putative ligand binding site [chemical binding]; other site 504832009181 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 504832009182 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832009183 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 504832009184 putative dimerization interface [polypeptide binding]; other site 504832009185 Protein of unknown function DUF72; Region: DUF72; pfam01904 504832009186 Low affinity iron permease; Region: Iron_permease; pfam04120 504832009187 Isochorismatase family; Region: Isochorismatase; pfam00857 504832009188 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 504832009189 catalytic triad [active] 504832009190 conserved cis-peptide bond; other site 504832009191 short chain dehydrogenase; Provisional; Region: PRK06701 504832009192 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 504832009193 NAD binding site [chemical binding]; other site 504832009194 metal binding site [ion binding]; metal-binding site 504832009195 active site 504832009196 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 504832009197 active site 504832009198 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 504832009199 Ligand Binding Site [chemical binding]; other site 504832009200 Molecular Tunnel; other site 504832009201 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 504832009202 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 504832009203 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832009204 Walker A/P-loop; other site 504832009205 ATP binding site [chemical binding]; other site 504832009206 Q-loop/lid; other site 504832009207 ABC transporter signature motif; other site 504832009208 Walker B; other site 504832009209 D-loop; other site 504832009210 H-loop/switch region; other site 504832009211 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 504832009212 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 504832009213 S-adenosylmethionine binding site [chemical binding]; other site 504832009214 Histidine kinase; Region: HisKA_3; pfam07730 504832009215 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 504832009216 ATP binding site [chemical binding]; other site 504832009217 Mg2+ binding site [ion binding]; other site 504832009218 G-X-G motif; other site 504832009219 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 504832009220 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832009221 active site 504832009222 phosphorylation site [posttranslational modification] 504832009223 intermolecular recognition site; other site 504832009224 dimerization interface [polypeptide binding]; other site 504832009225 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 504832009226 DNA binding residues [nucleotide binding] 504832009227 dimerization interface [polypeptide binding]; other site 504832009228 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 504832009229 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 504832009230 Walker A/P-loop; other site 504832009231 ATP binding site [chemical binding]; other site 504832009232 Q-loop/lid; other site 504832009233 ABC transporter signature motif; other site 504832009234 Walker B; other site 504832009235 D-loop; other site 504832009236 H-loop/switch region; other site 504832009237 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 504832009238 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 504832009239 Walker A/P-loop; other site 504832009240 ATP binding site [chemical binding]; other site 504832009241 Q-loop/lid; other site 504832009242 ABC transporter signature motif; other site 504832009243 Walker B; other site 504832009244 D-loop; other site 504832009245 H-loop/switch region; other site 504832009246 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 504832009247 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 504832009248 TM-ABC transporter signature motif; other site 504832009249 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 504832009250 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 504832009251 TM-ABC transporter signature motif; other site 504832009252 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 504832009253 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 504832009254 dimerization interface [polypeptide binding]; other site 504832009255 ligand binding site [chemical binding]; other site 504832009256 Transcriptional regulator [Transcription]; Region: IclR; COG1414 504832009257 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 504832009258 Bacterial transcriptional regulator; Region: IclR; pfam01614 504832009259 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832009260 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832009261 LysR substrate binding domain; Region: LysR_substrate; pfam03466 504832009262 dimerization interface [polypeptide binding]; other site 504832009263 Amino acid synthesis; Region: AA_synth; pfam06684 504832009264 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 504832009265 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 504832009266 tetrameric interface [polypeptide binding]; other site 504832009267 NAD binding site [chemical binding]; other site 504832009268 catalytic residues [active] 504832009269 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 504832009270 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 504832009271 metal binding site [ion binding]; metal-binding site 504832009272 active site 504832009273 I-site; other site 504832009274 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 504832009275 Uncharacterized conserved protein [Function unknown]; Region: COG3287 504832009276 FIST N domain; Region: FIST; pfam08495 504832009277 FIST C domain; Region: FIST_C; pfam10442 504832009278 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 504832009279 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 504832009280 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 504832009281 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 504832009282 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 504832009283 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 504832009284 catalytic loop [active] 504832009285 iron binding site [ion binding]; other site 504832009286 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 504832009287 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 504832009288 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 504832009289 Amidohydrolase; Region: Amidohydro_4; pfam13147 504832009290 active site 504832009291 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 504832009292 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009293 Walker A/P-loop; other site 504832009294 ATP binding site [chemical binding]; other site 504832009295 Q-loop/lid; other site 504832009296 ABC transporter signature motif; other site 504832009297 Walker B; other site 504832009298 D-loop; other site 504832009299 H-loop/switch region; other site 504832009300 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 504832009301 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 504832009302 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009303 Walker A/P-loop; other site 504832009304 ATP binding site [chemical binding]; other site 504832009305 Q-loop/lid; other site 504832009306 ABC transporter signature motif; other site 504832009307 Walker B; other site 504832009308 D-loop; other site 504832009309 H-loop/switch region; other site 504832009310 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832009311 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 504832009312 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 504832009313 dimer interface [polypeptide binding]; other site 504832009314 conserved gate region; other site 504832009315 putative PBP binding loops; other site 504832009316 ABC-ATPase subunit interface; other site 504832009317 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 504832009318 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 504832009319 dimer interface [polypeptide binding]; other site 504832009320 conserved gate region; other site 504832009321 putative PBP binding loops; other site 504832009322 ABC-ATPase subunit interface; other site 504832009323 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 504832009324 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 504832009325 Transcriptional regulators [Transcription]; Region: MarR; COG1846 504832009326 MarR family; Region: MarR_2; pfam12802 504832009327 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 504832009328 Amidase; Region: Amidase; cl11426 504832009329 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 504832009330 metal-binding site [ion binding] 504832009331 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832009332 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 504832009333 metal-binding site [ion binding] 504832009334 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832009335 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 504832009336 metal-binding site [ion binding] 504832009337 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832009338 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 504832009339 motif II; other site 504832009340 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 504832009341 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 504832009342 DNA binding residues [nucleotide binding] 504832009343 dimer interface [polypeptide binding]; other site 504832009344 copper binding site [ion binding]; other site 504832009345 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 504832009346 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009347 Walker A/P-loop; other site 504832009348 ATP binding site [chemical binding]; other site 504832009349 Q-loop/lid; other site 504832009350 ABC transporter signature motif; other site 504832009351 Walker B; other site 504832009352 D-loop; other site 504832009353 H-loop/switch region; other site 504832009354 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 504832009355 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 504832009356 Walker A/P-loop; other site 504832009357 ATP binding site [chemical binding]; other site 504832009358 Q-loop/lid; other site 504832009359 ABC transporter signature motif; other site 504832009360 Walker B; other site 504832009361 D-loop; other site 504832009362 H-loop/switch region; other site 504832009363 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 504832009364 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 504832009365 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_17; cd08503 504832009366 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 504832009367 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 504832009368 dimer interface [polypeptide binding]; other site 504832009369 conserved gate region; other site 504832009370 putative PBP binding loops; other site 504832009371 ABC-ATPase subunit interface; other site 504832009372 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 504832009373 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 504832009374 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 504832009375 dimer interface [polypeptide binding]; other site 504832009376 conserved gate region; other site 504832009377 putative PBP binding loops; other site 504832009378 ABC-ATPase subunit interface; other site 504832009379 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832009380 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 504832009381 ATP binding site [chemical binding]; other site 504832009382 Mg2+ binding site [ion binding]; other site 504832009383 G-X-G motif; other site 504832009384 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 504832009385 Ribonuclease P; Region: Ribonuclease_P; cl00457 504832009386 membrane protein insertase; Provisional; Region: PRK01318 504832009387 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 504832009388 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 504832009389 G1 box; other site 504832009390 GTP/Mg2+ binding site [chemical binding]; other site 504832009391 Switch I region; other site 504832009392 G2 box; other site 504832009393 G3 box; other site 504832009394 Switch II region; other site 504832009395 G4 box; other site 504832009396 G5 box; other site 504832009397 Uncharacterized small membrane protein [Function unknown]; Region: COG2363 504832009398 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 504832009399 feedback inhibition sensing region; other site 504832009400 homohexameric interface [polypeptide binding]; other site 504832009401 nucleotide binding site [chemical binding]; other site 504832009402 N-acetyl-L-glutamate binding site [chemical binding]; other site 504832009403 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 504832009404 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; cl17915 504832009405 motif II; other site 504832009406 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 504832009407 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 504832009408 trimer interface [polypeptide binding]; other site 504832009409 active site 504832009410 substrate binding site [chemical binding]; other site 504832009411 CoA binding site [chemical binding]; other site 504832009412 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 504832009413 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 504832009414 metal binding site [ion binding]; metal-binding site 504832009415 dimer interface [polypeptide binding]; other site 504832009416 nucleosidase; Provisional; Region: PRK05634 504832009417 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 504832009418 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 504832009419 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 504832009420 dimerization interface 3.5A [polypeptide binding]; other site 504832009421 active site 504832009422 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 504832009423 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 504832009424 putative active site [active] 504832009425 substrate binding site [chemical binding]; other site 504832009426 putative cosubstrate binding site; other site 504832009427 catalytic site [active] 504832009428 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 504832009429 substrate binding site [chemical binding]; other site 504832009430 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 504832009431 active site 504832009432 catalytic residues [active] 504832009433 metal binding site [ion binding]; metal-binding site 504832009434 RmuC family; Region: RmuC; pfam02646 504832009435 muropeptide transporter; Validated; Region: ampG; cl17669 504832009436 muropeptide transporter; Reviewed; Region: ampG; PRK11902 504832009437 recombination protein RecR; Reviewed; Region: recR; PRK00076 504832009438 RecR protein; Region: RecR; pfam02132 504832009439 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 504832009440 putative active site [active] 504832009441 putative metal-binding site [ion binding]; other site 504832009442 tetramer interface [polypeptide binding]; other site 504832009443 hypothetical protein; Validated; Region: PRK00153 504832009444 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 504832009445 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 504832009446 Walker A motif; other site 504832009447 ATP binding site [chemical binding]; other site 504832009448 Walker B motif; other site 504832009449 arginine finger; other site 504832009450 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 504832009451 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 504832009452 HIT domain; Region: HIT; pfam01230 504832009453 nucleotide binding site/active site [active] 504832009454 HIT family signature motif; other site 504832009455 catalytic residue [active] 504832009456 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 504832009457 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 504832009458 substrate binding site [chemical binding]; other site 504832009459 ATP binding site [chemical binding]; other site 504832009460 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 504832009461 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 504832009462 putative DNA binding site [nucleotide binding]; other site 504832009463 putative Zn2+ binding site [ion binding]; other site 504832009464 AsnC family; Region: AsnC_trans_reg; pfam01037 504832009465 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 504832009466 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832009467 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 504832009468 putative dimerization interface [polypeptide binding]; other site 504832009469 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 504832009470 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 504832009471 ligand binding site [chemical binding]; other site 504832009472 NAD binding site [chemical binding]; other site 504832009473 dimerization interface [polypeptide binding]; other site 504832009474 catalytic site [active] 504832009475 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 504832009476 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 504832009477 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 504832009478 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 504832009479 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 504832009480 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 504832009481 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 504832009482 DNA-binding site [nucleotide binding]; DNA binding site 504832009483 UTRA domain; Region: UTRA; pfam07702 504832009484 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 504832009485 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 504832009486 active site 504832009487 substrate binding site [chemical binding]; other site 504832009488 metal binding site [ion binding]; metal-binding site 504832009489 Protein of unknown function (DUF938); Region: DUF938; pfam06080 504832009490 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 504832009491 catalytic motif [active] 504832009492 Catalytic residue [active] 504832009493 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 504832009494 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 504832009495 ATP binding site [chemical binding]; other site 504832009496 putative Mg++ binding site [ion binding]; other site 504832009497 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 504832009498 nucleotide binding region [chemical binding]; other site 504832009499 ATP-binding site [chemical binding]; other site 504832009500 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 504832009501 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 504832009502 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 504832009503 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 504832009504 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 504832009505 Predicted membrane protein [Function unknown]; Region: COG4763 504832009506 Acyltransferase family; Region: Acyl_transf_3; pfam01757 504832009507 5'-3' exonuclease; Region: 53EXOc; smart00475 504832009508 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 504832009509 active site 504832009510 metal binding site 1 [ion binding]; metal-binding site 504832009511 putative 5' ssDNA interaction site; other site 504832009512 metal binding site 3; metal-binding site 504832009513 metal binding site 2 [ion binding]; metal-binding site 504832009514 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 504832009515 putative DNA binding site [nucleotide binding]; other site 504832009516 putative metal binding site [ion binding]; other site 504832009517 DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]; Region: PolA; COG0749 504832009518 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 504832009519 active site 504832009520 catalytic site [active] 504832009521 substrate binding site [chemical binding]; other site 504832009522 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 504832009523 active site 504832009524 DNA binding site [nucleotide binding] 504832009525 catalytic site [active] 504832009526 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 504832009527 active site 504832009528 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 504832009529 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 504832009530 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 504832009531 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 504832009532 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 504832009533 active site 504832009534 substrate-binding site [chemical binding]; other site 504832009535 metal-binding site [ion binding] 504832009536 ATP binding site [chemical binding]; other site 504832009537 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 504832009538 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 504832009539 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 504832009540 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 504832009541 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 504832009542 active site 504832009543 phosphorylation site [posttranslational modification] 504832009544 intermolecular recognition site; other site 504832009545 dimerization interface [polypeptide binding]; other site 504832009546 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 504832009547 DNA binding site [nucleotide binding] 504832009548 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 504832009549 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 504832009550 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 504832009551 HAMP domain; Region: HAMP; pfam00672 504832009552 dimerization interface [polypeptide binding]; other site 504832009553 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 504832009554 dimer interface [polypeptide binding]; other site 504832009555 phosphorylation site [posttranslational modification] 504832009556 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 504832009557 ATP binding site [chemical binding]; other site 504832009558 Mg2+ binding site [ion binding]; other site 504832009559 G-X-G motif; other site 504832009560 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 504832009561 Hpr binding site; other site 504832009562 active site 504832009563 homohexamer subunit interaction site [polypeptide binding]; other site 504832009564 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 504832009565 active pocket/dimerization site; other site 504832009566 active site 504832009567 phosphorylation site [posttranslational modification] 504832009568 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 504832009569 dimerization domain swap beta strand [polypeptide binding]; other site 504832009570 regulatory protein interface [polypeptide binding]; other site 504832009571 active site 504832009572 regulatory phosphorylation site [posttranslational modification]; other site 504832009573 GTP-binding protein LepA; Provisional; Region: PRK05433 504832009574 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 504832009575 G1 box; other site 504832009576 putative GEF interaction site [polypeptide binding]; other site 504832009577 GTP/Mg2+ binding site [chemical binding]; other site 504832009578 Switch I region; other site 504832009579 G2 box; other site 504832009580 G3 box; other site 504832009581 Switch II region; other site 504832009582 G4 box; other site 504832009583 G5 box; other site 504832009584 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 504832009585 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 504832009586 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 504832009587 Uncharacterized conserved protein [Function unknown]; Region: COG3422 504832009588 penicillin-insensitive murein endopeptidase; Reviewed; Region: mepA; PRK09429 504832009589 molybdenum-pterin binding domain; Region: Mop; TIGR00638 504832009590 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 504832009591 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 504832009592 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 504832009593 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 504832009594 dimer interface [polypeptide binding]; other site 504832009595 conserved gate region; other site 504832009596 putative PBP binding loops; other site 504832009597 ABC-ATPase subunit interface; other site 504832009598 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 504832009599 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 504832009600 Walker A/P-loop; other site 504832009601 ATP binding site [chemical binding]; other site 504832009602 Q-loop/lid; other site 504832009603 ABC transporter signature motif; other site 504832009604 Walker B; other site 504832009605 D-loop; other site 504832009606 H-loop/switch region; other site 504832009607 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 504832009608 intersubunit interface [polypeptide binding]; other site 504832009609 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 504832009610 ABC-ATPase subunit interface; other site 504832009611 dimer interface [polypeptide binding]; other site 504832009612 putative PBP binding regions; other site 504832009613 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 504832009614 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 504832009615 Walker A/P-loop; other site 504832009616 ATP binding site [chemical binding]; other site 504832009617 Q-loop/lid; other site 504832009618 ABC transporter signature motif; other site 504832009619 Walker B; other site 504832009620 D-loop; other site 504832009621 H-loop/switch region; other site 504832009622 potassium/proton antiporter; Reviewed; Region: PRK05326 504832009623 Transporter associated domain; Region: CorC_HlyC; smart01091 504832009624 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 504832009625 Mechanosensitive ion channel; Region: MS_channel; pfam00924 504832009626 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 504832009627 active site 504832009628 hypothetical protein; Reviewed; Region: PRK00024 504832009629 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 504832009630 MPN+ (JAMM) motif; other site 504832009631 Zinc-binding site [ion binding]; other site 504832009632 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 504832009633 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 504832009634 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 504832009635 active site 504832009636 DNA binding site [nucleotide binding] 504832009637 Int/Topo IB signature motif; other site 504832009638 Immunoglobulin domain; Region: Ig; cl11960 504832009639 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 504832009640 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 504832009641 VirB7 interaction site; other site 504832009642 conjugal transfer protein TrbF; Provisional; Region: PRK13872 504832009643 conjugal transfer protein TrbL; Provisional; Region: PRK13875 504832009644 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 504832009645 conjugative transfer region protein TrbK; Region: other_trbK; TIGR04360 504832009646 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 504832009647 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 504832009648 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 504832009649 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 504832009650 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 504832009651 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 504832009652 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 504832009653 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 504832009654 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 504832009655 Walker A motif; other site 504832009656 ATP binding site [chemical binding]; other site 504832009657 Walker B motif; other site 504832009658 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 504832009659 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 504832009660 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 504832009661 Walker A motif; other site 504832009662 ATP binding site [chemical binding]; other site 504832009663 Walker B motif; other site 504832009664 Transcriptional regulator [Transcription]; Region: LysR; COG0583 504832009665 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 504832009666 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 504832009667 dimerization interface [polypeptide binding]; other site 504832009668 substrate binding pocket [chemical binding]; other site 504832009669 RNA polymerase sigma factor; Provisional; Region: PRK12539 504832009670 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832009671 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 504832009672 DNA binding residues [nucleotide binding] 504832009673 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 504832009674 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 504832009675 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 504832009676 E3 interaction surface; other site 504832009677 lipoyl attachment site [posttranslational modification]; other site 504832009678 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832009679 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 504832009680 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 504832009681 Predicted metal-binding protein [General function prediction only]; Region: COG3019 504832009682 Copper resistance protein D; Region: CopD; cl00563 504832009683 Domain of unknown function (DUF4396); Region: DUF4396; pfam14342 504832009684 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 504832009685 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832009686 Multicopper oxidase; Region: Cu-oxidase; pfam00394 504832009687 OpgC protein; Region: OpgC_C; pfam10129 504832009688 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 504832009689 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 504832009690 Coenzyme A binding pocket [chemical binding]; other site 504832009691 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 504832009692 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 504832009693 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 504832009694 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 504832009695 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 504832009696 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832009697 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 504832009698 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 504832009699 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 504832009700 putative homodimer interface [polypeptide binding]; other site 504832009701 putative homotetramer interface [polypeptide binding]; other site 504832009702 putative allosteric switch controlling residues; other site 504832009703 putative metal binding site [ion binding]; other site 504832009704 putative homodimer-homodimer interface [polypeptide binding]; other site 504832009705 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832009706 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 504832009707 motif II; other site 504832009708 Autoinducer binding domain; Region: Autoind_bind; pfam03472 504832009709 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 504832009710 DNA binding residues [nucleotide binding] 504832009711 dimerization interface [polypeptide binding]; other site 504832009712 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 504832009713 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 504832009714 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 504832009715 P-loop; other site 504832009716 Magnesium ion binding site [ion binding]; other site 504832009717 replication initiation protein RepC; Provisional; Region: PRK13824 504832009718 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 504832009719 putative DNA binding site [nucleotide binding]; other site 504832009720 Replication protein C C-terminal region; Region: RP-C_C; pfam11800 504832009721 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 504832009722 non-specific DNA binding site [nucleotide binding]; other site 504832009723 salt bridge; other site 504832009724 sequence-specific DNA binding site [nucleotide binding]; other site 504832009725 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 504832009726 dimer interface [polypeptide binding]; other site 504832009727 ssDNA binding site [nucleotide binding]; other site 504832009728 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832009729 replication initiation protein RepC; Provisional; Region: PRK13824 504832009730 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 504832009731 putative DNA binding site [nucleotide binding]; other site 504832009732 Replication protein C C-terminal region; Region: RP-C_C; pfam11800 504832009733 plasmid partitioning protein RepB; Region: partition_RepB; TIGR03454 504832009734 ParB-like nuclease domain; Region: ParBc; pfam02195 504832009735 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 504832009736 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 504832009737 DNA binding residues [nucleotide binding] 504832009738 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 504832009739 P-loop; other site 504832009740 Magnesium ion binding site [ion binding]; other site 504832009741 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 504832009742 Magnesium ion binding site [ion binding]; other site 504832009743 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 504832009744 active site 504832009745 DNA binding site [nucleotide binding] 504832009746 Int/Topo IB signature motif; other site 504832009747 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 504832009748 oligomeric interface; other site 504832009749 putative active site [active] 504832009750 homodimer interface [polypeptide binding]; other site 504832009751 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 504832009752 Protein of unknown function (DUF1612); Region: DUF1612; pfam07756 504832009753 HTH DNA binding domain; Region: HTH_13; pfam11972 504832009754 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 504832009755 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 504832009756 Walker A motif; other site 504832009757 ATP binding site [chemical binding]; other site 504832009758 Walker B motif; other site 504832009759 arginine finger; other site 504832009760 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 504832009761 active site 504832009762 catalytic triad [active] 504832009763 PLD-like domain; Region: PLDc_2; pfam13091 504832009764 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cd00138 504832009765 putative active site [active] 504832009766 catalytic site [active] 504832009767 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 504832009768 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 504832009769 ATP-binding site [chemical binding]; other site 504832009770 Methyltransferase domain; Region: Methyltransf_26; pfam13659 504832009771 putative regulator PrlF; Provisional; Region: PRK09974 504832009772 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 504832009773 Protein of unknown function (DUF736); Region: DUF736; pfam05284 504832009774 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 504832009775 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 504832009776 plasmid partitioning protein; Provisional; Region: PRK13832 504832009777 ParB-like nuclease domain; Region: ParB; smart00470 504832009778 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 504832009779 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 504832009780 S-adenosylmethionine binding site [chemical binding]; other site 504832009781 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 504832009782 DEAD-like helicases superfamily; Region: DEXDc; smart00487 504832009783 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 504832009784 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 504832009785 helicase superfamily c-terminal domain; Region: HELICc; smart00490 504832009786 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 504832009787 Protein of unknown function (DUF1419); Region: DUF1419; pfam07215 504832009788 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 504832009789 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cd00188 504832009790 active site 504832009791 metal binding site [ion binding]; metal-binding site 504832009792 RES domain; Region: RES; pfam08808 504832009793 Autoinducer synthetase; Region: Autoind_synth; cl17404 504832009794 hypothetical protein; Provisional; Region: PRK06518 504832009795 Staphylococcal nuclease homologues; Region: SNc; smart00318 504832009796 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 504832009797 dimer interface [polypeptide binding]; other site 504832009798 ssDNA binding site [nucleotide binding]; other site 504832009799 tetramer (dimer of dimers) interface [polypeptide binding]; other site 504832009800 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 504832009801 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 504832009802 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 504832009803 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 504832009804 N-acetyl-D-glucosamine binding site [chemical binding]; other site 504832009805 catalytic residue [active] 504832009806 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 504832009807 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 504832009808 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 504832009809 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 504832009810 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 504832009811 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 504832009812 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 504832009813 VirB7 interaction site; other site 504832009814 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 504832009815 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 504832009816 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 504832009817 Walker A motif; other site 504832009818 hexamer interface [polypeptide binding]; other site 504832009819 ATP binding site [chemical binding]; other site 504832009820 Walker B motif; other site 504832009821 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 504832009822 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 504832009823 Walker A motif; other site 504832009824 ATP binding site [chemical binding]; other site 504832009825 Walker B motif; other site 504832009826 EamA-like transporter family; Region: EamA; pfam00892 504832009827 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 504832009828 EamA-like transporter family; Region: EamA; pfam00892 504832009829 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 504832009830 TPR repeat; Region: TPR_11; pfam13414 504832009831 TPR repeat; Region: TPR_11; pfam13414 504832009832 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 504832009833 binding surface 504832009834 TPR motif; other site 504832009835 TPR repeat; Region: TPR_11; pfam13414 504832009836 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 504832009837 binding surface 504832009838 TPR motif; other site 504832009839 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 504832009840 binding surface 504832009841 TPR repeat; Region: TPR_11; pfam13414 504832009842 TPR motif; other site 504832009843 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 504832009844 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 504832009845 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 504832009846 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 504832009847 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 504832009848 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 504832009849 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 504832009850 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12689 504832009851 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 504832009852 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 504832009853 Cytochrome c; Region: Cytochrom_C; pfam00034 504832009854 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 504832009855 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 504832009856 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832009857 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832009858 Soluble P-type ATPase [General function prediction only]; Region: COG4087 504832009859 OpgC protein; Region: OpgC_C; pfam10129 504832009860 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 504832009861 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 504832009862 E3 interaction surface; other site 504832009863 lipoyl attachment site [posttranslational modification]; other site 504832009864 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832009865 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 504832009866 PilZ domain; Region: PilZ; pfam07238 504832009867 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 504832009868 Nitrogen regulatory protein P-II; Region: P-II; cl00412 504832009869 Nitrogen regulatory protein P-II; Region: P-II; smart00938 504832009870 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 504832009871 lipoyl-biotinyl attachment site [posttranslational modification]; other site 504832009872 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832009873 Outer membrane efflux protein; Region: OEP; pfam02321 504832009874 Outer membrane efflux protein; Region: OEP; pfam02321 504832009875 Major Facilitator Superfamily; Region: MFS_1; pfam07690 504832009876 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 504832009877 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 504832009878 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 504832009879 putative DNA binding site [nucleotide binding]; other site 504832009880 putative Zn2+ binding site [ion binding]; other site 504832009881 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 504832009882 Low molecular weight phosphatase family; Region: LMWPc; cd00115 504832009883 active site 504832009884 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 504832009885 Sodium Bile acid symporter family; Region: SBF; cl17470 504832009886 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 504832009887 ArsC family; Region: ArsC; pfam03960 504832009888 catalytic residues [active] 504832009889 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 504832009890 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 504832009891 mercuric reductase; Region: MerA; TIGR02053 504832009892 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 504832009893 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 504832009894 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 504832009895 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 504832009896 metal-binding site [ion binding] 504832009897 MerT mercuric transport protein; Region: MerT; cl03578 504832009898 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 504832009899 DNA binding residues [nucleotide binding] 504832009900 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 504832009901 dimer interface [polypeptide binding]; other site 504832009902 putative metal binding site [ion binding]; other site 504832009903 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 504832009904 Cation efflux family; Region: Cation_efflux; pfam01545 504832009905 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 504832009906 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 504832009907 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 504832009908 metal-binding site [ion binding] 504832009909 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 504832009910 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 504832009911 metal-binding site [ion binding] 504832009912 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 504832009913 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 504832009914 motif II; other site 504832009915 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 504832009916 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 504832009917 putative substrate translocation pore; other site 504832009918 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 504832009919 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 504832009920 DNA binding residues [nucleotide binding] 504832009921 dimer interface [polypeptide binding]; other site 504832009922 metal binding site [ion binding]; metal-binding site 504832009923 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 504832009924 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 504832009925 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 504832009926 metal-binding site [ion binding] 504832009927 OpgC protein; Region: OpgC_C; pfam10129 504832009928 Acyltransferase family; Region: Acyl_transf_3; pfam01757 504832009929 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 504832009930 RNA polymerase sigma factor; Provisional; Region: PRK12539 504832009931 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 504832009932 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 504832009933 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 504832009934 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 504832009935 HlyD family secretion protein; Region: HlyD_3; pfam13437 504832009936 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 504832009937 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 504832009938 multicopper oxidase; Provisional; Region: PRK10965 504832009939 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 504832009940 Multicopper oxidase; Region: Cu-oxidase; pfam00394 504832009941 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 504832009942 Protein of unknown function, DUF; Region: DUF411; cl01142