-- dump date 20140618_194209 -- class Genbank::misc_feature -- table misc_feature_note -- id note 187272000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 187272000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 187272000003 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 187272000004 ATP-binding site [chemical binding]; other site 187272000005 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 187272000006 Walker A motif; other site 187272000007 ATP binding site [chemical binding]; other site 187272000008 Walker B motif; other site 187272000009 arginine finger; other site 187272000010 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 187272000011 DnaA box-binding interface [nucleotide binding]; other site 187272000012 DNA polymerase III subunit beta; Validated; Region: PRK05643 187272000013 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 187272000014 putative DNA binding surface [nucleotide binding]; other site 187272000015 dimer interface [polypeptide binding]; other site 187272000016 beta-clamp/clamp loader binding surface; other site 187272000017 beta-clamp/translesion DNA polymerase binding surface; other site 187272000018 recombination protein F; Reviewed; Region: recF; PRK00064 187272000019 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272000020 Walker A/P-loop; other site 187272000021 ATP binding site [chemical binding]; other site 187272000022 Q-loop/lid; other site 187272000023 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272000024 ABC transporter signature motif; other site 187272000025 Walker B; other site 187272000026 D-loop; other site 187272000027 H-loop/switch region; other site 187272000028 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 187272000029 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272000030 Mg2+ binding site [ion binding]; other site 187272000031 G-X-G motif; other site 187272000032 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 187272000033 anchoring element; other site 187272000034 dimer interface [polypeptide binding]; other site 187272000035 ATP binding site [chemical binding]; other site 187272000036 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 187272000037 active site 187272000038 putative metal-binding site [ion binding]; other site 187272000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 187272000040 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 187272000041 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 187272000042 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 187272000043 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 187272000044 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 187272000045 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 187272000046 active site 187272000047 homotetramer interface [polypeptide binding]; other site 187272000048 glucokinase, proteobacterial type; Region: glk; TIGR00749 187272000049 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 187272000050 nucleotide binding site [chemical binding]; other site 187272000051 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 187272000052 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 187272000053 putative acyl-acceptor binding pocket; other site 187272000054 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 187272000055 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 187272000056 active site 187272000057 motif I; other site 187272000058 motif II; other site 187272000059 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 187272000060 DALR anticodon binding domain; Region: DALR_1; smart00836 187272000061 anticodon binding site; other site 187272000062 tRNA binding surface [nucleotide binding]; other site 187272000063 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 187272000064 dimer interface [polypeptide binding]; other site 187272000065 motif 1; other site 187272000066 active site 187272000067 motif 2; other site 187272000068 motif 3; other site 187272000069 glutamine synthetase; Provisional; Region: glnA; PRK09469 187272000070 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 187272000071 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 187272000072 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 187272000073 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 187272000074 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 187272000075 putative active site [active] 187272000076 heme pocket [chemical binding]; other site 187272000077 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 187272000078 dimer interface [polypeptide binding]; other site 187272000079 phosphorylation site [posttranslational modification] 187272000080 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272000081 ATP binding site [chemical binding]; other site 187272000082 Mg2+ binding site [ion binding]; other site 187272000083 G-X-G motif; other site 187272000084 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 187272000085 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272000086 active site 187272000087 phosphorylation site [posttranslational modification] 187272000088 intermolecular recognition site; other site 187272000089 dimerization interface [polypeptide binding]; other site 187272000090 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 187272000091 Walker A motif; other site 187272000092 ATP binding site [chemical binding]; other site 187272000093 Walker B motif; other site 187272000094 arginine finger; other site 187272000095 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272000096 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 187272000097 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 187272000098 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 187272000099 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 187272000100 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 187272000101 ring oligomerisation interface [polypeptide binding]; other site 187272000102 ATP/Mg binding site [chemical binding]; other site 187272000103 stacking interactions; other site 187272000104 hinge regions; other site 187272000105 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 187272000106 oligomerisation interface [polypeptide binding]; other site 187272000107 mobile loop; other site 187272000108 roof hairpin; other site 187272000109 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 187272000110 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 187272000111 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 187272000112 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 187272000113 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 187272000114 DsbD alpha interface [polypeptide binding]; other site 187272000115 catalytic residues [active] 187272000116 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 187272000117 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272000118 catalytic residues [active] 187272000119 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 187272000120 Dehydroquinase class II; Region: DHquinase_II; pfam01220 187272000121 active site 187272000122 trimer interface [polypeptide binding]; other site 187272000123 dimer interface [polypeptide binding]; other site 187272000124 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 187272000125 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 187272000126 carboxyltransferase (CT) interaction site; other site 187272000127 biotinylation site [posttranslational modification]; other site 187272000128 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 187272000129 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 187272000130 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 187272000131 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 187272000132 YfaZ precursor; Region: YfaZ; pfam07437 187272000133 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 187272000134 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 187272000135 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 187272000136 putative NAD(P) binding site [chemical binding]; other site 187272000137 active site 187272000138 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 187272000139 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 187272000140 active site 187272000141 NTP binding site [chemical binding]; other site 187272000142 metal binding triad [ion binding]; metal-binding site 187272000143 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 187272000144 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 187272000145 Zn2+ binding site [ion binding]; other site 187272000146 Mg2+ binding site [ion binding]; other site 187272000147 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 187272000148 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 187272000149 active site 187272000150 catalytic tetrad [active] 187272000151 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 187272000152 S-adenosylmethionine binding site [chemical binding]; other site 187272000153 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 187272000154 ThiS interaction site; other site 187272000155 putative active site [active] 187272000156 tetramer interface [polypeptide binding]; other site 187272000157 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 187272000158 thiS-thiF/thiG interaction site; other site 187272000159 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 187272000160 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 187272000161 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 187272000162 Protein of unknown function (DUF770); Region: DUF770; pfam05591 187272000163 type VI secretion protein, EvpB/VC_A0108 family; Region: VI_chp_2; TIGR03355 187272000164 Protein of unknown function (DUF877); Region: DUF877; pfam05943 187272000165 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 187272000166 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 187272000167 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 187272000168 Protein of unknown function (DUF1305); Region: DUF1305; pfam06996 187272000169 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 187272000170 phosphopeptide binding site; other site 187272000171 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 187272000172 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522 187272000173 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 187272000174 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 187272000175 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 187272000176 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 187272000177 Walker A motif; other site 187272000178 ATP binding site [chemical binding]; other site 187272000179 Walker B motif; other site 187272000180 arginine finger; other site 187272000181 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272000182 Protein of unknown function (DUF3121); Region: DUF3121; pfam11319 187272000183 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 187272000184 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 187272000185 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 187272000186 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 187272000187 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 187272000188 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 187272000189 PAAR motif; Region: PAAR_motif; pfam05488 187272000190 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 187272000191 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 187272000192 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 187272000193 Protein of unknown function, DUF484; Region: DUF484; cl17449 187272000194 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 187272000195 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 187272000196 active site 187272000197 Int/Topo IB signature motif; other site 187272000198 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272000199 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272000200 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 187272000201 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 187272000202 NADP binding site [chemical binding]; other site 187272000203 dimer interface [polypeptide binding]; other site 187272000204 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 187272000205 active site 187272000206 HslU subunit interaction site [polypeptide binding]; other site 187272000207 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 187272000208 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 187272000209 Walker A motif; other site 187272000210 ATP binding site [chemical binding]; other site 187272000211 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 187272000212 Walker B motif; other site 187272000213 arginine finger; other site 187272000214 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 187272000215 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 187272000216 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 187272000217 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 187272000218 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 187272000219 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 187272000220 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 187272000221 arginine decarboxylase; Provisional; Region: PRK05354 187272000222 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 187272000223 active site 187272000224 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 187272000225 catalytic residues [active] 187272000226 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 187272000227 spermidine synthase; Provisional; Region: PRK00811 187272000228 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 187272000229 S-adenosylmethionine binding site [chemical binding]; other site 187272000230 PAS fold; Region: PAS_3; pfam08447 187272000231 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 187272000232 putative active site [active] 187272000233 heme pocket [chemical binding]; other site 187272000234 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272000235 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 187272000236 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 187272000237 PAS domain; Region: PAS_9; pfam13426 187272000238 putative active site [active] 187272000239 heme pocket [chemical binding]; other site 187272000240 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272000241 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272000242 metal binding site [ion binding]; metal-binding site 187272000243 active site 187272000244 I-site; other site 187272000245 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 187272000246 Double zinc ribbon; Region: DZR; pfam12773 187272000247 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 187272000248 RDD family; Region: RDD; pfam06271 187272000249 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 187272000250 putative ABC transporter ATP-binding protein YbbL; Provisional; Region: PRK10247 187272000251 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 187272000252 Walker A/P-loop; other site 187272000253 ATP binding site [chemical binding]; other site 187272000254 Q-loop/lid; other site 187272000255 ABC transporter signature motif; other site 187272000256 Walker B; other site 187272000257 D-loop; other site 187272000258 H-loop/switch region; other site 187272000259 Bacterial transcriptional activator domain; Region: BTAD; smart01043 187272000260 TOMM system kinase/cyclase fusion protein; Region: TOMM_kin_cyc; TIGR03903 187272000261 AAA ATPase domain; Region: AAA_16; pfam13191 187272000262 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 187272000263 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 187272000264 Nitrogen regulatory protein P-II; Region: P-II; smart00938 187272000265 Membrane fusogenic activity; Region: BMFP; pfam04380 187272000266 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 187272000267 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 187272000268 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 187272000269 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 187272000270 Cytochrome c; Region: Cytochrom_C; cl11414 187272000271 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 187272000272 feedback inhibition sensing region; other site 187272000273 homohexameric interface [polypeptide binding]; other site 187272000274 nucleotide binding site [chemical binding]; other site 187272000275 N-acetyl-L-glutamate binding site [chemical binding]; other site 187272000276 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 187272000277 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 187272000278 tetramer (dimer of dimers) interface [polypeptide binding]; other site 187272000279 active site 187272000280 dimer interface [polypeptide binding]; other site 187272000281 threonine dehydratase; Reviewed; Region: PRK09224 187272000282 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 187272000283 tetramer interface [polypeptide binding]; other site 187272000284 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272000285 catalytic residue [active] 187272000286 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 187272000287 putative Ile/Val binding site [chemical binding]; other site 187272000288 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 187272000289 putative Ile/Val binding site [chemical binding]; other site 187272000290 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272000291 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272000292 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 187272000293 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 187272000294 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 187272000295 FAD binding pocket [chemical binding]; other site 187272000296 FAD binding motif [chemical binding]; other site 187272000297 phosphate binding motif [ion binding]; other site 187272000298 beta-alpha-beta structure motif; other site 187272000299 NAD binding pocket [chemical binding]; other site 187272000300 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 187272000301 Major Facilitator Superfamily; Region: MFS_1; pfam07690 187272000302 putative substrate translocation pore; other site 187272000303 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 187272000304 transcriptional activator RfaH; Region: RfaH; TIGR01955 187272000305 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 187272000306 heterodimer interface [polypeptide binding]; other site 187272000307 homodimer interface [polypeptide binding]; other site 187272000308 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 187272000309 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 187272000310 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 187272000311 ATP binding site [chemical binding]; other site 187272000312 substrate interface [chemical binding]; other site 187272000313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 187272000314 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 187272000315 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272000316 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272000317 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 187272000318 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 187272000319 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 187272000320 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 187272000321 Substrate binding site; other site 187272000322 Cupin domain; Region: Cupin_2; cl17218 187272000323 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 187272000324 PqqD family protein, HPr-rel-A system; Region: PqqD_rel_X; TIGR04353 187272000325 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 187272000326 Methyltransferase domain; Region: Methyltransf_31; pfam13847 187272000327 S-adenosylmethionine binding site [chemical binding]; other site 187272000328 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 187272000329 VanZ like family; Region: VanZ; cl01971 187272000330 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 187272000331 active site 187272000332 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 187272000333 homodimer interface [polypeptide binding]; other site 187272000334 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 187272000335 Inorganic pyrophosphatase; Region: Pyrophosphatase; pfam00719 187272000336 dimer interface [polypeptide binding]; other site 187272000337 substrate binding site [chemical binding]; other site 187272000338 metal binding sites [ion binding]; metal-binding site 187272000339 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u9; cd10933 187272000340 putative active site [active] 187272000341 putative catalytic site [active] 187272000342 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 187272000343 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 187272000344 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 187272000345 active site 187272000346 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 187272000347 Transposase; Region: DDE_Tnp_ISL3; pfam01610 187272000348 O-Antigen ligase; Region: Wzy_C; cl04850 187272000349 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 187272000350 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 187272000351 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272000352 Walker A/P-loop; other site 187272000353 ATP binding site [chemical binding]; other site 187272000354 Q-loop/lid; other site 187272000355 ABC transporter signature motif; other site 187272000356 Walker B; other site 187272000357 D-loop; other site 187272000358 H-loop/switch region; other site 187272000359 acyl-CoA ligase (AMP-forming), exosortase A-associated; Region: ligase_PEP_1; TIGR03098 187272000360 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272000361 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_6; cd05922 187272000362 acyl-activating enzyme (AAE) consensus motif; other site 187272000363 acyl-activating enzyme (AAE) consensus motif; other site 187272000364 putative AMP binding site [chemical binding]; other site 187272000365 putative active site [active] 187272000366 putative CoA binding site [chemical binding]; other site 187272000367 pyridoxal-dependent decarboxylase, exosortase A system-associated; Region: dCO2ase_PEP1; TIGR03099 187272000368 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase; Region: PLPDE_III_Btrk_like; cd06839 187272000369 dimer interface [polypeptide binding]; other site 187272000370 active site 187272000371 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 187272000372 catalytic residues [active] 187272000373 substrate binding site [chemical binding]; other site 187272000374 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 187272000375 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 187272000376 exosortase A system-associated hydrolase 1; Region: hydr1_PEP; TIGR03100 187272000377 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272000378 Transposase [DNA replication, recombination, and repair]; Region: COG5421 187272000379 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 187272000380 Amidinotransferase; Region: Amidinotransf; pfam02274 187272000381 D-alanine:D-alanyl carrier protein ligase (DltA); Region: DltA; cd05945 187272000382 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 187272000383 acyl-activating enzyme (AAE) consensus motif; other site 187272000384 AMP binding site [chemical binding]; other site 187272000385 exosortase A system-associated hydrolase 2; Region: hydr2_PEP; TIGR03101 187272000386 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272000387 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 187272000388 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 187272000389 active site 187272000390 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 187272000391 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 187272000392 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 187272000393 Ligand Binding Site [chemical binding]; other site 187272000394 Molecular Tunnel; other site 187272000395 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 187272000396 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272000397 AMP binding site [chemical binding]; other site 187272000398 active site 187272000399 acyl-activating enzyme (AAE) consensus motif; other site 187272000400 CoA binding site [chemical binding]; other site 187272000401 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 187272000402 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272000403 PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family; Region: stp3; TIGR04063 187272000404 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 187272000405 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 187272000406 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 187272000407 active site 187272000408 dimer interface [polypeptide binding]; other site 187272000409 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 187272000410 Ligand Binding Site [chemical binding]; other site 187272000411 Molecular Tunnel; other site 187272000412 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 187272000413 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 187272000414 putative ADP-binding pocket [chemical binding]; other site 187272000415 exosortase A; Region: exosortase_1; TIGR03109 187272000416 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 187272000417 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 187272000418 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 187272000419 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 187272000420 FemAB-related protein, PEP-CTERM system-associated; Region: pepcterm_femAB; TIGR03019 187272000421 polysaccharide deacetylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 187272000422 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 187272000423 putative active site [active] 187272000424 putative catalytic site [active] 187272000425 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 187272000426 AAA ATPase domain; Region: AAA_16; pfam13191 187272000427 uncharacterized protein, PEP-CTERM system associated; Region: pepcterm_hypo_1; TIGR03016 187272000428 uncharacterized protein, PEP-CTERM system associated; Region: pepcterm_hypo_1; TIGR03016 187272000429 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 187272000430 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 187272000431 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 187272000432 Chain length determinant protein; Region: Wzz; pfam02706 187272000433 PilZ domain; Region: PilZ; pfam07238 187272000434 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 187272000435 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 187272000436 hypothetical protein; Validated; Region: PRK08223 187272000437 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 187272000438 ATP binding site [chemical binding]; other site 187272000439 substrate interface [chemical binding]; other site 187272000440 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 187272000441 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 187272000442 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 187272000443 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 187272000444 binding surface 187272000445 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 187272000446 TPR motif; other site 187272000447 binding surface 187272000448 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 187272000449 binding surface 187272000450 TPR motif; other site 187272000451 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 187272000452 TPR motif; other site 187272000453 binding surface 187272000454 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 187272000455 TPR motif; other site 187272000456 binding surface 187272000457 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 187272000458 TPR motif; other site 187272000459 binding surface 187272000460 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 187272000461 TPR motif; other site 187272000462 binding surface 187272000463 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 187272000464 TPR motif; other site 187272000465 binding surface 187272000466 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 187272000467 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272000468 active site 187272000469 phosphorylation site [posttranslational modification] 187272000470 intermolecular recognition site; other site 187272000471 dimerization interface [polypeptide binding]; other site 187272000472 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 187272000473 Walker A motif; other site 187272000474 ATP binding site [chemical binding]; other site 187272000475 Walker B motif; other site 187272000476 arginine finger; other site 187272000477 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272000478 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 187272000479 GAF domain; Region: GAF_3; pfam13492 187272000480 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272000481 ATP binding site [chemical binding]; other site 187272000482 Mg2+ binding site [ion binding]; other site 187272000483 G-X-G motif; other site 187272000484 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 187272000485 Bacterial sugar transferase; Region: Bac_transf; pfam02397 187272000486 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 187272000487 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 187272000488 SLBB domain; Region: SLBB; pfam10531 187272000489 PilZ domain; Region: PilZ; pfam07238 187272000490 Uncharacterized conserved protein [Function unknown]; Region: COG1434 187272000491 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 187272000492 putative active site [active] 187272000493 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 187272000494 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 187272000495 NAD binding site [chemical binding]; other site 187272000496 homodimer interface [polypeptide binding]; other site 187272000497 active site 187272000498 substrate binding site [chemical binding]; other site 187272000499 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 187272000500 PAS domain; Region: PAS_9; pfam13426 187272000501 putative active site [active] 187272000502 heme pocket [chemical binding]; other site 187272000503 PAS domain S-box; Region: sensory_box; TIGR00229 187272000504 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 187272000505 putative active site [active] 187272000506 heme pocket [chemical binding]; other site 187272000507 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272000508 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272000509 metal binding site [ion binding]; metal-binding site 187272000510 active site 187272000511 I-site; other site 187272000512 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 187272000513 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 187272000514 dimerization interface [polypeptide binding]; other site 187272000515 domain crossover interface; other site 187272000516 redox-dependent activation switch; other site 187272000517 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 187272000518 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 187272000519 GatB domain; Region: GatB_Yqey; smart00845 187272000520 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 187272000521 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 187272000522 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 187272000523 rod shape-determining protein MreB; Provisional; Region: PRK13927 187272000524 MreB and similar proteins; Region: MreB_like; cd10225 187272000525 nucleotide binding site [chemical binding]; other site 187272000526 Mg binding site [ion binding]; other site 187272000527 putative protofilament interaction site [polypeptide binding]; other site 187272000528 RodZ interaction site [polypeptide binding]; other site 187272000529 rod shape-determining protein MreC; Provisional; Region: PRK13922 187272000530 rod shape-determining protein MreC; Region: MreC; pfam04085 187272000531 rod shape-determining protein MreD; Region: MreD; cl01087 187272000532 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 187272000533 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 187272000534 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 187272000535 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 187272000536 Transglycosylase SLT domain; Region: SLT_2; pfam13406 187272000537 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 187272000538 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272000539 catalytic residue [active] 187272000540 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 187272000541 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 187272000542 Sporulation related domain; Region: SPOR; pfam05036 187272000543 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 187272000544 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 187272000545 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 187272000546 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 187272000547 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 187272000548 homodimer interface [polypeptide binding]; other site 187272000549 substrate-cofactor binding pocket; other site 187272000550 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272000551 catalytic residue [active] 187272000552 Protein of unknown function (DUF493); Region: DUF493; pfam04359 187272000553 lipoate-protein ligase B; Provisional; Region: PRK14342 187272000554 UreD urease accessory protein; Region: UreD; pfam01774 187272000555 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 187272000556 alpha-gamma subunit interface [polypeptide binding]; other site 187272000557 beta-gamma subunit interface [polypeptide binding]; other site 187272000558 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 187272000559 gamma-beta subunit interface [polypeptide binding]; other site 187272000560 alpha-beta subunit interface [polypeptide binding]; other site 187272000561 urease subunit alpha; Reviewed; Region: ureC; PRK13207 187272000562 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 187272000563 subunit interactions [polypeptide binding]; other site 187272000564 active site 187272000565 flap region; other site 187272000566 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 187272000567 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 187272000568 dimer interface [polypeptide binding]; other site 187272000569 catalytic residues [active] 187272000570 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 187272000571 UreF; Region: UreF; pfam01730 187272000572 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 187272000573 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 187272000574 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 187272000575 putative ligand binding site [chemical binding]; other site 187272000576 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 187272000577 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 187272000578 TM-ABC transporter signature motif; other site 187272000579 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 187272000580 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 187272000581 TM-ABC transporter signature motif; other site 187272000582 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 187272000583 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 187272000584 Walker A/P-loop; other site 187272000585 ATP binding site [chemical binding]; other site 187272000586 Q-loop/lid; other site 187272000587 ABC transporter signature motif; other site 187272000588 Walker B; other site 187272000589 D-loop; other site 187272000590 H-loop/switch region; other site 187272000591 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 187272000592 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 187272000593 Walker A/P-loop; other site 187272000594 ATP binding site [chemical binding]; other site 187272000595 Q-loop/lid; other site 187272000596 ABC transporter signature motif; other site 187272000597 Walker B; other site 187272000598 D-loop; other site 187272000599 H-loop/switch region; other site 187272000600 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 187272000601 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 187272000602 putative substrate translocation pore; other site 187272000603 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 187272000604 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 187272000605 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_6; cd06256 187272000606 putative active site [active] 187272000607 Zn binding site [ion binding]; other site 187272000608 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 187272000609 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 187272000610 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 187272000611 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 187272000612 Substrate binding site; other site 187272000613 metal-binding site 187272000614 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 187272000615 Phosphotransferase enzyme family; Region: APH; pfam01636 187272000616 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 187272000617 Organic solvent tolerance protein; Region: OstA_C; pfam04453 187272000618 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 187272000619 SurA N-terminal domain; Region: SurA_N; pfam09312 187272000620 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 187272000621 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 187272000622 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 187272000623 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 187272000624 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 187272000625 MoaE interaction surface [polypeptide binding]; other site 187272000626 MoeB interaction surface [polypeptide binding]; other site 187272000627 thiocarboxylated glycine; other site 187272000628 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 187272000629 phosphoglycerate transporter family protein; Region: 2A0104; TIGR00881 187272000630 putative substrate translocation pore; other site 187272000631 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 187272000632 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 187272000633 putative active site [active] 187272000634 Zn binding site [ion binding]; other site 187272000635 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 187272000636 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 187272000637 trimer interface [polypeptide binding]; other site 187272000638 putative metal binding site [ion binding]; other site 187272000639 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 187272000640 Ligand Binding Site [chemical binding]; other site 187272000641 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 187272000642 Ligand Binding Site [chemical binding]; other site 187272000643 Cupin domain; Region: Cupin_2; cl17218 187272000644 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272000645 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272000646 diaminopimelate decarboxylase; Region: lysA; TIGR01048 187272000647 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 187272000648 active site 187272000649 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 187272000650 substrate binding site [chemical binding]; other site 187272000651 catalytic residues [active] 187272000652 dimer interface [polypeptide binding]; other site 187272000653 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; pfam13627 187272000654 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 187272000655 putative hydrolase; Provisional; Region: PRK11460 187272000656 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 187272000657 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 187272000658 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 187272000659 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 187272000660 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 187272000661 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 187272000662 4Fe-4S binding domain; Region: Fer4; pfam00037 187272000663 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 187272000664 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 187272000665 molybdopterin cofactor binding site; other site 187272000666 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 187272000667 molybdopterin cofactor binding site; other site 187272000668 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 187272000669 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 187272000670 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 187272000671 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 187272000672 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 187272000673 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 187272000674 dimer interface [polypeptide binding]; other site 187272000675 phosphorylation site [posttranslational modification] 187272000676 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272000677 ATP binding site [chemical binding]; other site 187272000678 Mg2+ binding site [ion binding]; other site 187272000679 G-X-G motif; other site 187272000680 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272000681 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272000682 active site 187272000683 phosphorylation site [posttranslational modification] 187272000684 intermolecular recognition site; other site 187272000685 dimerization interface [polypeptide binding]; other site 187272000686 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 187272000687 Walker A motif; other site 187272000688 ATP binding site [chemical binding]; other site 187272000689 Walker B motif; other site 187272000690 arginine finger; other site 187272000691 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272000692 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 187272000693 putative active site [active] 187272000694 transaldolase; Provisional; Region: PRK03903 187272000695 catalytic residue [active] 187272000696 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 187272000697 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 187272000698 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 187272000699 active site 187272000700 metal binding site [ion binding]; metal-binding site 187272000701 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 187272000702 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 187272000703 amidase catalytic site [active] 187272000704 substrate binding site [chemical binding]; other site 187272000705 Zn binding residues [ion binding]; other site 187272000706 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 187272000707 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 187272000708 catalytic residues [active] 187272000709 Transcriptional regulator; Region: Rrf2; cl17282 187272000710 Rrf2 family protein; Region: rrf2_super; TIGR00738 187272000711 NnrS protein; Region: NnrS; cl01258 187272000712 NnrS protein; Region: NnrS; pfam05940 187272000713 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 187272000714 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 187272000715 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 187272000716 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 187272000717 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 187272000718 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 187272000719 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 187272000720 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 187272000721 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 187272000722 Cytochrome c [Energy production and conversion]; Region: COG3258 187272000723 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 187272000724 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 187272000725 active site 187272000726 FMN binding site [chemical binding]; other site 187272000727 substrate binding site [chemical binding]; other site 187272000728 3Fe-4S cluster binding site [ion binding]; other site 187272000729 DoxX; Region: DoxX; cl17842 187272000730 Tubulin-tyrosine ligase family; Region: TTL; pfam03133 187272000731 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 187272000732 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 187272000733 binding surface 187272000734 TPR motif; other site 187272000735 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272000736 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 187272000737 ligand binding site [chemical binding]; other site 187272000738 translocation protein TolB; Provisional; Region: tolB; PRK04922 187272000739 TolB amino-terminal domain; Region: TolB_N; pfam04052 187272000740 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 187272000741 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 187272000742 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 187272000743 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 187272000744 TolA protein; Region: tolA_full; TIGR02794 187272000745 TonB C terminal; Region: TonB_2; pfam13103 187272000746 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 187272000747 TolR protein; Region: tolR; TIGR02801 187272000748 TolQ protein; Region: tolQ; TIGR02796 187272000749 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 187272000750 Malic enzyme, N-terminal domain; Region: malic; pfam00390 187272000751 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 187272000752 putative NAD(P) binding site [chemical binding]; other site 187272000753 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 187272000754 thioredoxin reductase; Provisional; Region: PRK10262 187272000755 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272000756 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272000757 Pilin (bacterial filament); Region: Pilin; pfam00114 187272000758 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 187272000759 active site 187272000760 NTP binding site [chemical binding]; other site 187272000761 metal binding triad [ion binding]; metal-binding site 187272000762 antibiotic binding site [chemical binding]; other site 187272000763 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 187272000764 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 187272000765 Pilin (bacterial filament); Region: Pilin; pfam00114 187272000766 Type II transport protein GspH; Region: GspH; pfam12019 187272000767 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 187272000768 PilX N-terminal; Region: PilX_N; pfam14341 187272000769 Domain of unknown function (DUF4399); Region: DUF4399; pfam14347 187272000770 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272000771 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272000772 active site 187272000773 phosphorylation site [posttranslational modification] 187272000774 intermolecular recognition site; other site 187272000775 dimerization interface [polypeptide binding]; other site 187272000776 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 187272000777 Walker A motif; other site 187272000778 ATP binding site [chemical binding]; other site 187272000779 Walker B motif; other site 187272000780 arginine finger; other site 187272000781 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272000782 active site 187272000783 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 187272000784 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 187272000785 isocitrate dehydrogenase; Validated; Region: PRK07362 187272000786 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 187272000787 FOG: CBS domain [General function prediction only]; Region: COG0517 187272000788 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_17; cd04630 187272000789 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272000790 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272000791 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 187272000792 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 187272000793 S-adenosylmethionine binding site [chemical binding]; other site 187272000794 Protein of unknown function (DUF502); Region: DUF502; cl01107 187272000795 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 187272000796 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 187272000797 dimer interface [polypeptide binding]; other site 187272000798 TPP-binding site [chemical binding]; other site 187272000799 Transketolase, pyrimidine binding domain; Region: Transket_pyr; smart00861 187272000800 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 187272000801 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 187272000802 E3 interaction surface; other site 187272000803 lipoyl attachment site [posttranslational modification]; other site 187272000804 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 187272000805 E3 interaction surface; other site 187272000806 lipoyl attachment site [posttranslational modification]; other site 187272000807 e3 binding domain; Region: E3_binding; pfam02817 187272000808 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 187272000809 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 187272000810 E3 interaction surface; other site 187272000811 lipoyl attachment site [posttranslational modification]; other site 187272000812 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 187272000813 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272000814 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272000815 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272000816 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 187272000817 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 187272000818 Trm112p-like protein; Region: Trm112p; cl01066 187272000819 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 187272000820 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 187272000821 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 187272000822 Walker A motif; other site 187272000823 ATP binding site [chemical binding]; other site 187272000824 Walker B motif; other site 187272000825 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 187272000826 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 187272000827 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 187272000828 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 187272000829 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 187272000830 active site 187272000831 metal binding site [ion binding]; metal-binding site 187272000832 hexamer interface [polypeptide binding]; other site 187272000833 peptide chain release factor 1; Validated; Region: prfA; PRK00591 187272000834 This domain is found in peptide chain release factors; Region: PCRF; smart00937 187272000835 RF-1 domain; Region: RF-1; pfam00472 187272000836 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 187272000837 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 187272000838 tRNA; other site 187272000839 putative tRNA binding site [nucleotide binding]; other site 187272000840 putative NADP binding site [chemical binding]; other site 187272000841 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 187272000842 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 187272000843 TPR motif; other site 187272000844 binding surface 187272000845 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 187272000846 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 187272000847 binding surface 187272000848 TPR motif; other site 187272000849 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 187272000850 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 187272000851 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 187272000852 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 187272000853 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 187272000854 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 187272000855 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272000856 active site 187272000857 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 187272000858 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 187272000859 5S rRNA interface [nucleotide binding]; other site 187272000860 CTC domain interface [polypeptide binding]; other site 187272000861 L16 interface [polypeptide binding]; other site 187272000862 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 187272000863 putative active site [active] 187272000864 catalytic residue [active] 187272000865 GTP-binding protein YchF; Reviewed; Region: PRK09601 187272000866 YchF GTPase; Region: YchF; cd01900 187272000867 G1 box; other site 187272000868 GTP/Mg2+ binding site [chemical binding]; other site 187272000869 Switch I region; other site 187272000870 G2 box; other site 187272000871 Switch II region; other site 187272000872 G3 box; other site 187272000873 G4 box; other site 187272000874 G5 box; other site 187272000875 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 187272000876 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 187272000877 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 187272000878 SlyX; Region: SlyX; pfam04102 187272000879 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 187272000880 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 187272000881 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 187272000882 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 187272000883 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 187272000884 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 187272000885 active site 187272000886 dimer interface [polypeptide binding]; other site 187272000887 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 187272000888 dimer interface [polypeptide binding]; other site 187272000889 active site 187272000890 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 187272000891 Protein of unknown function (DUF815); Region: DUF815; pfam05673 187272000892 Walker A motif; other site 187272000893 ATP binding site [chemical binding]; other site 187272000894 Walker B motif; other site 187272000895 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 187272000896 AAA domain; Region: AAA_26; pfam13500 187272000897 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 187272000898 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 187272000899 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 187272000900 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 187272000901 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 187272000902 Subunit I/III interface [polypeptide binding]; other site 187272000903 D-pathway; other site 187272000904 Subunit I/VIIc interface [polypeptide binding]; other site 187272000905 Subunit I/IV interface [polypeptide binding]; other site 187272000906 Subunit I/II interface [polypeptide binding]; other site 187272000907 Low-spin heme (heme a) binding site [chemical binding]; other site 187272000908 Subunit I/VIIa interface [polypeptide binding]; other site 187272000909 Subunit I/VIa interface [polypeptide binding]; other site 187272000910 Dimer interface; other site 187272000911 Putative water exit pathway; other site 187272000912 Binuclear center (heme a3/CuB) [ion binding]; other site 187272000913 K-pathway; other site 187272000914 Subunit I/Vb interface [polypeptide binding]; other site 187272000915 Putative proton exit pathway; other site 187272000916 Subunit I/VIb interface; other site 187272000917 Subunit I/VIc interface [polypeptide binding]; other site 187272000918 Electron transfer pathway; other site 187272000919 Subunit I/VIIIb interface [polypeptide binding]; other site 187272000920 Subunit I/VIIb interface [polypeptide binding]; other site 187272000921 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 187272000922 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 187272000923 Subunit III/VIIa interface [polypeptide binding]; other site 187272000924 Phospholipid binding site [chemical binding]; other site 187272000925 Subunit I/III interface [polypeptide binding]; other site 187272000926 Subunit III/VIb interface [polypeptide binding]; other site 187272000927 Subunit III/VIa interface; other site 187272000928 Subunit III/Vb interface [polypeptide binding]; other site 187272000929 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 187272000930 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 187272000931 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 187272000932 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 187272000933 UbiA prenyltransferase family; Region: UbiA; pfam01040 187272000934 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 187272000935 putative active site pocket [active] 187272000936 dimerization interface [polypeptide binding]; other site 187272000937 putative catalytic residue [active] 187272000938 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 187272000939 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 187272000940 VacJ like lipoprotein; Region: VacJ; cl01073 187272000941 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 187272000942 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 187272000943 FAD binding domain; Region: FAD_binding_4; pfam01565 187272000944 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 187272000945 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 187272000946 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 187272000947 putative active site [active] 187272000948 catalytic site [active] 187272000949 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 187272000950 putative active site [active] 187272000951 catalytic site [active] 187272000952 BCCT family transporter; Region: BCCT; pfam02028 187272000953 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 187272000954 metal binding site 2 [ion binding]; metal-binding site 187272000955 putative DNA binding helix; other site 187272000956 metal binding site 1 [ion binding]; metal-binding site 187272000957 dimer interface [polypeptide binding]; other site 187272000958 structural Zn2+ binding site [ion binding]; other site 187272000959 LabA_like proteins; Region: LabA; cd10911 187272000960 putative metal binding site [ion binding]; other site 187272000961 Uncharacterized conserved protein [Function unknown]; Region: COG1432 187272000962 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 187272000963 DTAP/Switch II; other site 187272000964 Switch I; other site 187272000965 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 187272000966 Carbon starvation protein CstA; Region: CstA; pfam02554 187272000967 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 187272000968 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 187272000969 Ligand Binding Site [chemical binding]; other site 187272000970 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 187272000971 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 187272000972 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 187272000973 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 187272000974 S-adenosylmethionine binding site [chemical binding]; other site 187272000975 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 187272000976 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 187272000977 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 187272000978 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 187272000979 ligand binding site [chemical binding]; other site 187272000980 flexible hinge region; other site 187272000981 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 187272000982 non-specific DNA interactions [nucleotide binding]; other site 187272000983 DNA binding site [nucleotide binding] 187272000984 sequence specific DNA binding site [nucleotide binding]; other site 187272000985 putative cAMP binding site [chemical binding]; other site 187272000986 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 187272000987 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 187272000988 putative dimer interface [polypeptide binding]; other site 187272000989 Ion transport protein; Region: Ion_trans; pfam00520 187272000990 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 187272000991 metal-binding site [ion binding] 187272000992 Thermus thermophilus CsoR, a Cu(I)-sensing transcriptional regulator, and related domains; this domain family was previously known as part of DUF156; Region: TthCsoR-like_DUF156; cd10151 187272000993 putative homotetramer interface [polypeptide binding]; other site 187272000994 putative homodimer interface [polypeptide binding]; other site 187272000995 allosteric switch controlling residues; other site 187272000996 putative metal binding site [ion binding]; other site 187272000997 putative homodimer-homodimer interface [polypeptide binding]; other site 187272000998 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 187272000999 metal-binding site [ion binding] 187272001000 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 187272001001 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 187272001002 metal-binding site [ion binding] 187272001003 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 187272001004 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 187272001005 motif II; other site 187272001006 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 187272001007 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 187272001008 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 187272001009 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272001010 catalytic residue [active] 187272001011 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 187272001012 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272001013 ligand binding site [chemical binding]; other site 187272001014 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 187272001015 CPxP motif; other site 187272001016 Phasin protein; Region: Phasin_2; cl11491 187272001017 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 187272001018 putative inner membrane peptidase; Provisional; Region: PRK11778 187272001019 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 187272001020 tandem repeat interface [polypeptide binding]; other site 187272001021 oligomer interface [polypeptide binding]; other site 187272001022 active site residues [active] 187272001023 ORF6N domain; Region: ORF6N; pfam10543 187272001024 Predicted ATPase [General function prediction only]; Region: COG1485 187272001025 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 187272001026 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 187272001027 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 187272001028 putative active site [active] 187272001029 Zn binding site [ion binding]; other site 187272001030 spermidine synthase; Provisional; Region: PRK00811 187272001031 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 187272001032 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 187272001033 S-adenosylmethionine binding site [chemical binding]; other site 187272001034 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 187272001035 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 187272001036 YGGT family; Region: YGGT; pfam02325 187272001037 YGGT family; Region: YGGT; pfam02325 187272001038 pyrroline-5-carboxylate reductase; Region: PLN02688 187272001039 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 187272001040 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 187272001041 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 187272001042 catalytic residue [active] 187272001043 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 187272001044 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 187272001045 Walker A motif; other site 187272001046 ATP binding site [chemical binding]; other site 187272001047 Walker B motif; other site 187272001048 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 187272001049 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 187272001050 Walker A motif; other site 187272001051 ATP binding site [chemical binding]; other site 187272001052 Walker B motif; other site 187272001053 dihydroorotase; Provisional; Region: PRK07627 187272001054 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 187272001055 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 187272001056 active site 187272001057 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 187272001058 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 187272001059 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 187272001060 bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase; Provisional; Region: PRK05205 187272001061 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 187272001062 hypothetical protein; Validated; Region: PRK00228 187272001063 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 187272001064 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 187272001065 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 187272001066 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 187272001067 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 187272001068 ApbE family; Region: ApbE; pfam02424 187272001069 glutathione synthetase; Provisional; Region: PRK05246 187272001070 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 187272001071 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 187272001072 Response regulator receiver domain; Region: Response_reg; pfam00072 187272001073 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272001074 active site 187272001075 phosphorylation site [posttranslational modification] 187272001076 intermolecular recognition site; other site 187272001077 dimerization interface [polypeptide binding]; other site 187272001078 Response regulator receiver domain; Region: Response_reg; pfam00072 187272001079 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272001080 active site 187272001081 phosphorylation site [posttranslational modification] 187272001082 intermolecular recognition site; other site 187272001083 dimerization interface [polypeptide binding]; other site 187272001084 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 187272001085 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 187272001086 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 187272001087 dimer interface [polypeptide binding]; other site 187272001088 putative CheW interface [polypeptide binding]; other site 187272001089 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 187272001090 putative binding surface; other site 187272001091 active site 187272001092 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 187272001093 putative binding surface; other site 187272001094 active site 187272001095 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 187272001096 putative binding surface; other site 187272001097 active site 187272001098 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 187272001099 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 187272001100 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272001101 ATP binding site [chemical binding]; other site 187272001102 Mg2+ binding site [ion binding]; other site 187272001103 G-X-G motif; other site 187272001104 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 187272001105 Response regulator receiver domain; Region: Response_reg; pfam00072 187272001106 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272001107 active site 187272001108 phosphorylation site [posttranslational modification] 187272001109 intermolecular recognition site; other site 187272001110 dimerization interface [polypeptide binding]; other site 187272001111 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 187272001112 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 187272001113 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK07030 187272001114 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 187272001115 inhibitor-cofactor binding pocket; inhibition site 187272001116 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272001117 catalytic residue [active] 187272001118 N-acetylglutamate synthase; Validated; Region: PRK05279 187272001119 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 187272001120 putative feedback inhibition sensing region; other site 187272001121 putative nucleotide binding site [chemical binding]; other site 187272001122 putative substrate binding site [chemical binding]; other site 187272001123 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272001124 Coenzyme A binding pocket [chemical binding]; other site 187272001125 acetylornithine deacetylase; Provisional; Region: PRK05111 187272001126 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 187272001127 metal binding site [ion binding]; metal-binding site 187272001128 putative dimer interface [polypeptide binding]; other site 187272001129 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 187272001130 Bacterial SH3 domain homologues; Region: SH3b; smart00287 187272001131 5' nucleotidase family; Region: 5_nucleotid; cl17687 187272001132 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 187272001133 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 187272001134 putative RNA binding site [nucleotide binding]; other site 187272001135 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 187272001136 S-adenosylmethionine binding site [chemical binding]; other site 187272001137 transcription termination factor Rho; Provisional; Region: rho; PRK09376 187272001138 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 187272001139 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 187272001140 RNA binding site [nucleotide binding]; other site 187272001141 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 187272001142 multimer interface [polypeptide binding]; other site 187272001143 Walker A motif; other site 187272001144 ATP binding site [chemical binding]; other site 187272001145 Walker B motif; other site 187272001146 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 187272001147 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272001148 catalytic residues [active] 187272001149 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 187272001150 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 187272001151 motif II; other site 187272001152 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 187272001153 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 187272001154 dimer interface [polypeptide binding]; other site 187272001155 ADP-ribose binding site [chemical binding]; other site 187272001156 active site 187272001157 nudix motif; other site 187272001158 metal binding site [ion binding]; metal-binding site 187272001159 thymidylate synthase; Reviewed; Region: thyA; PRK01827 187272001160 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 187272001161 dimerization interface [polypeptide binding]; other site 187272001162 active site 187272001163 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 187272001164 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 187272001165 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 187272001166 dimer interface [polypeptide binding]; other site 187272001167 active site 187272001168 glycine-pyridoxal phosphate binding site [chemical binding]; other site 187272001169 folate binding site [chemical binding]; other site 187272001170 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 187272001171 ATP cone domain; Region: ATP-cone; pfam03477 187272001172 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 187272001173 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 187272001174 catalytic motif [active] 187272001175 Zn binding site [ion binding]; other site 187272001176 RibD C-terminal domain; Region: RibD_C; cl17279 187272001177 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 187272001178 Lumazine binding domain; Region: Lum_binding; pfam00677 187272001179 Lumazine binding domain; Region: Lum_binding; pfam00677 187272001180 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 187272001181 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 187272001182 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 187272001183 dimerization interface [polypeptide binding]; other site 187272001184 active site 187272001185 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 187272001186 homopentamer interface [polypeptide binding]; other site 187272001187 active site 187272001188 transcription antitermination factor NusB; Region: nusB; TIGR01951 187272001189 thiamine monophosphate kinase; Provisional; Region: PRK05731 187272001190 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 187272001191 ATP binding site [chemical binding]; other site 187272001192 dimerization interface [polypeptide binding]; other site 187272001193 Methyltransferase domain; Region: Methyltransf_23; pfam13489 187272001194 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 187272001195 S-adenosylmethionine binding site [chemical binding]; other site 187272001196 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 187272001197 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 187272001198 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 187272001199 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 187272001200 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 187272001201 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 187272001202 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 187272001203 active site 187272001204 NTP binding site [chemical binding]; other site 187272001205 metal binding triad [ion binding]; metal-binding site 187272001206 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 187272001207 Transposase [DNA replication, recombination, and repair]; Region: COG5421 187272001208 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 187272001209 tetramer interfaces [polypeptide binding]; other site 187272001210 binuclear metal-binding site [ion binding]; other site 187272001211 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272001212 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 187272001213 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 187272001214 Walker A/P-loop; other site 187272001215 ATP binding site [chemical binding]; other site 187272001216 Q-loop/lid; other site 187272001217 ABC transporter signature motif; other site 187272001218 Walker B; other site 187272001219 D-loop; other site 187272001220 H-loop/switch region; other site 187272001221 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 187272001222 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 187272001223 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 187272001224 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 187272001225 FeS/SAM binding site; other site 187272001226 TRAM domain; Region: TRAM; pfam01938 187272001227 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 187272001228 PhoH-like protein; Region: PhoH; pfam02562 187272001229 metal-binding heat shock protein; Provisional; Region: PRK00016 187272001230 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 187272001231 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 187272001232 Transporter associated domain; Region: CorC_HlyC; smart01091 187272001233 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 187272001234 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 187272001235 putative active site [active] 187272001236 catalytic triad [active] 187272001237 putative dimer interface [polypeptide binding]; other site 187272001238 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 187272001239 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 187272001240 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 187272001241 HIGH motif; other site 187272001242 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 187272001243 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272001244 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272001245 active site 187272001246 KMSKS motif; other site 187272001247 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 187272001248 tRNA binding surface [nucleotide binding]; other site 187272001249 Lipopolysaccharide-assembly; Region: LptE; pfam04390 187272001250 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 187272001251 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 187272001252 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 187272001253 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 187272001254 putative catalytic cysteine [active] 187272001255 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 187272001256 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 187272001257 active site 187272001258 (T/H)XGH motif; other site 187272001259 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 187272001260 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 187272001261 Hemerythrin; Region: Hemerythrin; cd12107 187272001262 Fe binding site [ion binding]; other site 187272001263 Maf-like protein; Region: Maf; pfam02545 187272001264 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 187272001265 active site 187272001266 dimer interface [polypeptide binding]; other site 187272001267 ribonuclease G; Provisional; Region: PRK11712 187272001268 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 187272001269 homodimer interface [polypeptide binding]; other site 187272001270 oligonucleotide binding site [chemical binding]; other site 187272001271 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 187272001272 TIGR02099 family protein; Region: TIGR02099 187272001273 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 187272001274 nitrilase; Region: PLN02798 187272001275 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 187272001276 putative active site [active] 187272001277 catalytic triad [active] 187272001278 dimer interface [polypeptide binding]; other site 187272001279 protease TldD; Provisional; Region: tldD; PRK10735 187272001280 peptidase PmbA; Provisional; Region: PRK11040 187272001281 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 187272001282 30S subunit binding site; other site 187272001283 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 187272001284 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 187272001285 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 187272001286 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 187272001287 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 187272001288 Methyltransferase domain; Region: Methyltransf_23; pfam13489 187272001289 Methyltransferase domain; Region: Methyltransf_12; pfam08242 187272001290 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 187272001291 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 187272001292 putative ADP-ribose binding site [chemical binding]; other site 187272001293 putative active site [active] 187272001294 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 187272001295 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 187272001296 folate binding site [chemical binding]; other site 187272001297 NADP+ binding site [chemical binding]; other site 187272001298 LrgB-like family; Region: LrgB; pfam04172 187272001299 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 187272001300 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 187272001301 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 187272001302 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 187272001303 putative active site [active] 187272001304 Ap4A binding site [chemical binding]; other site 187272001305 nudix motif; other site 187272001306 putative metal binding site [ion binding]; other site 187272001307 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 187272001308 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 187272001309 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 187272001310 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 187272001311 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 187272001312 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 187272001313 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 187272001314 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 187272001315 heme binding site [chemical binding]; other site 187272001316 ferroxidase pore; other site 187272001317 ferroxidase diiron center [ion binding]; other site 187272001318 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 187272001319 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 187272001320 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272001321 catalytic residues [active] 187272001322 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 187272001323 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 187272001324 Cl- selectivity filter; other site 187272001325 Cl- binding residues [ion binding]; other site 187272001326 pore gating glutamate residue; other site 187272001327 dimer interface [polypeptide binding]; other site 187272001328 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 187272001329 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 187272001330 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 187272001331 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 187272001332 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 187272001333 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 187272001334 Peptidase family M23; Region: Peptidase_M23; pfam01551 187272001335 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 187272001336 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 187272001337 active site 187272001338 HIGH motif; other site 187272001339 dimer interface [polypeptide binding]; other site 187272001340 KMSKS motif; other site 187272001341 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 187272001342 RNA binding surface [nucleotide binding]; other site 187272001343 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 187272001344 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 187272001345 active site 187272001346 metal binding site [ion binding]; metal-binding site 187272001347 Biotin operon repressor [Transcription]; Region: BirA; COG1654 187272001348 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 187272001349 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 187272001350 pantothenate kinase; Reviewed; Region: PRK13322 187272001351 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 187272001352 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 187272001353 elongation factor Tu; Reviewed; Region: PRK00049 187272001354 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 187272001355 G1 box; other site 187272001356 GEF interaction site [polypeptide binding]; other site 187272001357 GTP/Mg2+ binding site [chemical binding]; other site 187272001358 Switch I region; other site 187272001359 G2 box; other site 187272001360 G3 box; other site 187272001361 Switch II region; other site 187272001362 G4 box; other site 187272001363 G5 box; other site 187272001364 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 187272001365 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 187272001366 Antibiotic Binding Site [chemical binding]; other site 187272001367 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 187272001368 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 187272001369 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 187272001370 putative homodimer interface [polypeptide binding]; other site 187272001371 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 187272001372 heterodimer interface [polypeptide binding]; other site 187272001373 homodimer interface [polypeptide binding]; other site 187272001374 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 187272001375 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 187272001376 23S rRNA interface [nucleotide binding]; other site 187272001377 L7/L12 interface [polypeptide binding]; other site 187272001378 putative thiostrepton binding site; other site 187272001379 L25 interface [polypeptide binding]; other site 187272001380 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 187272001381 mRNA/rRNA interface [nucleotide binding]; other site 187272001382 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 187272001383 23S rRNA interface [nucleotide binding]; other site 187272001384 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 187272001385 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 187272001386 L11 interface [polypeptide binding]; other site 187272001387 putative EF-Tu interaction site [polypeptide binding]; other site 187272001388 putative EF-G interaction site [polypeptide binding]; other site 187272001389 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 187272001390 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 187272001391 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 187272001392 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 187272001393 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 187272001394 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 187272001395 RPB3 interaction site [polypeptide binding]; other site 187272001396 RPB1 interaction site [polypeptide binding]; other site 187272001397 RPB11 interaction site [polypeptide binding]; other site 187272001398 RPB10 interaction site [polypeptide binding]; other site 187272001399 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 187272001400 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 187272001401 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 187272001402 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 187272001403 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 187272001404 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 187272001405 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 187272001406 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 187272001407 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 187272001408 Apocytochrome F, C-terminal; Region: Apocytochr_F_C; cl03168 187272001409 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 187272001410 DNA binding site [nucleotide binding] 187272001411 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 187272001412 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 187272001413 S17 interaction site [polypeptide binding]; other site 187272001414 S8 interaction site; other site 187272001415 16S rRNA interaction site [nucleotide binding]; other site 187272001416 streptomycin interaction site [chemical binding]; other site 187272001417 23S rRNA interaction site [nucleotide binding]; other site 187272001418 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 187272001419 30S ribosomal protein S7; Validated; Region: PRK05302 187272001420 elongation factor G; Reviewed; Region: PRK00007 187272001421 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 187272001422 G1 box; other site 187272001423 putative GEF interaction site [polypeptide binding]; other site 187272001424 GTP/Mg2+ binding site [chemical binding]; other site 187272001425 Switch I region; other site 187272001426 G2 box; other site 187272001427 G3 box; other site 187272001428 Switch II region; other site 187272001429 G4 box; other site 187272001430 G5 box; other site 187272001431 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 187272001432 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 187272001433 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 187272001434 elongation factor Tu; Reviewed; Region: PRK00049 187272001435 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 187272001436 G1 box; other site 187272001437 GEF interaction site [polypeptide binding]; other site 187272001438 GTP/Mg2+ binding site [chemical binding]; other site 187272001439 Switch I region; other site 187272001440 G2 box; other site 187272001441 G3 box; other site 187272001442 Switch II region; other site 187272001443 G4 box; other site 187272001444 G5 box; other site 187272001445 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 187272001446 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 187272001447 Antibiotic Binding Site [chemical binding]; other site 187272001448 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 187272001449 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 187272001450 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 187272001451 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 187272001452 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 187272001453 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 187272001454 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 187272001455 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 187272001456 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 187272001457 protein-rRNA interface [nucleotide binding]; other site 187272001458 putative translocon binding site; other site 187272001459 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 187272001460 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 187272001461 G-X-X-G motif; other site 187272001462 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 187272001463 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 187272001464 23S rRNA interface [nucleotide binding]; other site 187272001465 5S rRNA interface [nucleotide binding]; other site 187272001466 putative antibiotic binding site [chemical binding]; other site 187272001467 L25 interface [polypeptide binding]; other site 187272001468 L27 interface [polypeptide binding]; other site 187272001469 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 187272001470 23S rRNA interface [nucleotide binding]; other site 187272001471 putative translocon interaction site; other site 187272001472 signal recognition particle (SRP54) interaction site; other site 187272001473 L23 interface [polypeptide binding]; other site 187272001474 trigger factor interaction site; other site 187272001475 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 187272001476 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 187272001477 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 187272001478 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 187272001479 RNA binding site [nucleotide binding]; other site 187272001480 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 187272001481 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 187272001482 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 187272001483 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 187272001484 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 187272001485 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 187272001486 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 187272001487 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 187272001488 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 187272001489 5S rRNA interface [nucleotide binding]; other site 187272001490 23S rRNA interface [nucleotide binding]; other site 187272001491 L5 interface [polypeptide binding]; other site 187272001492 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 187272001493 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 187272001494 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 187272001495 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 187272001496 23S rRNA binding site [nucleotide binding]; other site 187272001497 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 187272001498 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 187272001499 SecY translocase; Region: SecY; pfam00344 187272001500 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 187272001501 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 187272001502 30S ribosomal protein S13; Region: bact_S13; TIGR03631 187272001503 30S ribosomal protein S11; Validated; Region: PRK05309 187272001504 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 187272001505 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 187272001506 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 187272001507 RNA binding surface [nucleotide binding]; other site 187272001508 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 187272001509 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 187272001510 alphaNTD homodimer interface [polypeptide binding]; other site 187272001511 alphaNTD - beta interaction site [polypeptide binding]; other site 187272001512 alphaNTD - beta' interaction site [polypeptide binding]; other site 187272001513 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 187272001514 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 187272001515 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 187272001516 malate dehydrogenase; Provisional; Region: PRK05442 187272001517 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 187272001518 NAD(P) binding site [chemical binding]; other site 187272001519 dimer interface [polypeptide binding]; other site 187272001520 malate binding site [chemical binding]; other site 187272001521 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 187272001522 active site 187272001523 catalytic triad [active] 187272001524 oxyanion hole [active] 187272001525 switch loop; other site 187272001526 tartrate dehydrogenase; Region: TTC; TIGR02089 187272001527 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 187272001528 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 187272001529 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 187272001530 Beta-Casp domain; Region: Beta-Casp; smart01027 187272001531 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 187272001532 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 187272001533 4-aminobutyrate aminotransferase; Provisional; Region: PRK08117 187272001534 inhibitor-cofactor binding pocket; inhibition site 187272001535 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272001536 catalytic residue [active] 187272001537 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 187272001538 S-adenosylmethionine binding site [chemical binding]; other site 187272001539 Protein of unknown function (DUF2384); Region: DUF2384; cl17718 187272001540 RES domain; Region: RES; cl02411 187272001541 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 187272001542 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 187272001543 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 187272001544 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 187272001545 CopC domain; Region: CopC; pfam04234 187272001546 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 187272001547 HsdM N-terminal domain; Region: HsdM_N; pfam12161 187272001548 Methyltransferase domain; Region: Methyltransf_26; pfam13659 187272001549 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 187272001550 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 187272001551 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 187272001552 Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Poa1p_like; cd02901 187272001553 ADP-ribose binding site [chemical binding]; other site 187272001554 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 187272001555 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 187272001556 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 187272001557 ATP binding site [chemical binding]; other site 187272001558 putative Mg++ binding site [ion binding]; other site 187272001559 Protein of unknown function DUF45; Region: DUF45; pfam01863 187272001560 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 187272001561 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 187272001562 Fic family protein [Function unknown]; Region: COG3177 187272001563 Fic/DOC family; Region: Fic; pfam02661 187272001564 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 187272001565 dimerization interface [polypeptide binding]; other site 187272001566 putative Zn2+ binding site [ion binding]; other site 187272001567 putative DNA binding site [nucleotide binding]; other site 187272001568 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 187272001569 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 187272001570 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 187272001571 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 187272001572 catalytic residues [active] 187272001573 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 187272001574 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 187272001575 Domain of unknown function (DUF336); Region: DUF336; cl01249 187272001576 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 187272001577 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 187272001578 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 187272001579 active site 187272001580 substrate binding site [chemical binding]; other site 187272001581 cosubstrate binding site; other site 187272001582 catalytic site [active] 187272001583 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 187272001584 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 187272001585 dimerization interface [polypeptide binding]; other site 187272001586 putative ATP binding site [chemical binding]; other site 187272001587 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 187272001588 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 187272001589 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 187272001590 Walker A motif; other site 187272001591 ATP binding site [chemical binding]; other site 187272001592 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 187272001593 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 187272001594 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 187272001595 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 187272001596 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 187272001597 Transcriptional regulator; Region: Rrf2; cl17282 187272001598 Acylphosphatase; Region: Acylphosphatase; pfam00708 187272001599 Cytochrome c553 [Energy production and conversion]; Region: COG2863 187272001600 Cytochrome c553 [Energy production and conversion]; Region: COG2863 187272001601 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 187272001602 active site 187272001603 Subunit B of Class III Extradiol ring-cleavage dioxygenases; Region: Extradiol_Dioxygenase_3B_like; cl00599 187272001604 active site 187272001605 metal binding site [ion binding]; metal-binding site 187272001606 probable FeS assembly SUF system protein SufT; Region: FeS_long_SufT; TIGR03406 187272001607 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 187272001608 catalytic residues [active] 187272001609 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 187272001610 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39A; cd02549 187272001611 putative active site [active] 187272001612 Tetratricopeptide repeat; Region: TPR_12; pfam13424 187272001613 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 187272001614 TPR motif; other site 187272001615 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 187272001616 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272001617 Coenzyme A binding pocket [chemical binding]; other site 187272001618 Predicted amidohydrolase [General function prediction only]; Region: COG0388 187272001619 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 187272001620 putative active site [active] 187272001621 catalytic triad [active] 187272001622 putative dimer interface [polypeptide binding]; other site 187272001623 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 187272001624 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272001625 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272001626 Surface antigen; Region: Bac_surface_Ag; pfam01103 187272001627 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 187272001628 Family of unknown function (DUF490); Region: DUF490; pfam04357 187272001629 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 187272001630 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 187272001631 putative NAD(P) binding site [chemical binding]; other site 187272001632 tRNA guanosine-2'-O-methyltransferase; Provisional; Region: PRK11081 187272001633 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 187272001634 SpoU, rRNA methylase, C-terminal; Region: SpoU_methylas_C; pfam12105 187272001635 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 187272001636 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 187272001637 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272001638 catalytic residue [active] 187272001639 prolyl-tRNA synthetase; Provisional; Region: PRK09194 187272001640 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 187272001641 dimer interface [polypeptide binding]; other site 187272001642 motif 1; other site 187272001643 active site 187272001644 motif 2; other site 187272001645 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 187272001646 putative deacylase active site [active] 187272001647 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 187272001648 active site 187272001649 motif 3; other site 187272001650 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 187272001651 anticodon binding site; other site 187272001652 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272001653 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 187272001654 PAS domain; Region: PAS_9; pfam13426 187272001655 putative active site [active] 187272001656 heme pocket [chemical binding]; other site 187272001657 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272001658 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272001659 metal binding site [ion binding]; metal-binding site 187272001660 active site 187272001661 I-site; other site 187272001662 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 187272001663 Predicted membrane protein [Function unknown]; Region: COG3174 187272001664 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 187272001665 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 187272001666 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 187272001667 putative valine binding site [chemical binding]; other site 187272001668 dimer interface [polypeptide binding]; other site 187272001669 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 187272001670 ketol-acid reductoisomerase; Provisional; Region: PRK05479 187272001671 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 187272001672 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 187272001673 Phasin protein; Region: Phasin_2; cl11491 187272001674 Protein of unknown function (DUF3185); Region: DUF3185; pfam11381 187272001675 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 187272001676 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 187272001677 Peptidase family M48; Region: Peptidase_M48; cl12018 187272001678 2-isopropylmalate synthase; Validated; Region: PRK00915 187272001679 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 187272001680 active site 187272001681 catalytic residues [active] 187272001682 metal binding site [ion binding]; metal-binding site 187272001683 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 187272001684 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 187272001685 Fe-S cluster binding site [ion binding]; other site 187272001686 active site 187272001687 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 187272001688 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272001689 Coenzyme A binding pocket [chemical binding]; other site 187272001690 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 187272001691 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 187272001692 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 187272001693 HIGH motif; other site 187272001694 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 187272001695 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 187272001696 active site 187272001697 KMSKS motif; other site 187272001698 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 187272001699 tRNA binding surface [nucleotide binding]; other site 187272001700 anticodon binding site; other site 187272001701 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 187272001702 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 187272001703 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 187272001704 multifunctional aminopeptidase A; Provisional; Region: PRK00913 187272001705 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 187272001706 interface (dimer of trimers) [polypeptide binding]; other site 187272001707 Substrate-binding/catalytic site; other site 187272001708 Zn-binding sites [ion binding]; other site 187272001709 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 187272001710 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 187272001711 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 187272001712 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 187272001713 RDD family; Region: RDD; pfam06271 187272001714 poly(A) polymerase; Region: pcnB; TIGR01942 187272001715 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 187272001716 active site 187272001717 NTP binding site [chemical binding]; other site 187272001718 metal binding triad [ion binding]; metal-binding site 187272001719 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 187272001720 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 187272001721 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 187272001722 catalytic center binding site [active] 187272001723 ATP binding site [chemical binding]; other site 187272001724 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 187272001725 active site 187272001726 oligomerization interface [polypeptide binding]; other site 187272001727 metal binding site [ion binding]; metal-binding site 187272001728 Pantoate-beta-alanine ligase; Region: PanC; cd00560 187272001729 pantoate--beta-alanine ligase; Region: panC; TIGR00018 187272001730 active site 187272001731 ATP-binding site [chemical binding]; other site 187272001732 pantoate-binding site; other site 187272001733 HXXH motif; other site 187272001734 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 187272001735 tetramerization interface [polypeptide binding]; other site 187272001736 active site 187272001737 epoxyqueuosine reductase; Region: TIGR00276 187272001738 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 187272001739 Uncharacterized conserved protein [Function unknown]; Region: COG0062 187272001740 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 187272001741 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 187272001742 AMIN domain; Region: AMIN; pfam11741 187272001743 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 187272001744 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 187272001745 active site 187272001746 metal binding site [ion binding]; metal-binding site 187272001747 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272001748 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 187272001749 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 187272001750 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272001751 ATP binding site [chemical binding]; other site 187272001752 Mg2+ binding site [ion binding]; other site 187272001753 G-X-G motif; other site 187272001754 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 187272001755 ATP binding site [chemical binding]; other site 187272001756 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 187272001757 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 187272001758 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 187272001759 bacterial Hfq-like; Region: Hfq; cd01716 187272001760 hexamer interface [polypeptide binding]; other site 187272001761 Sm1 motif; other site 187272001762 RNA binding site [nucleotide binding]; other site 187272001763 Sm2 motif; other site 187272001764 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 187272001765 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 187272001766 HflX GTPase family; Region: HflX; cd01878 187272001767 G1 box; other site 187272001768 GTP/Mg2+ binding site [chemical binding]; other site 187272001769 Switch I region; other site 187272001770 G2 box; other site 187272001771 G3 box; other site 187272001772 Switch II region; other site 187272001773 G4 box; other site 187272001774 G5 box; other site 187272001775 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 187272001776 HflK protein; Region: hflK; TIGR01933 187272001777 FtsH protease regulator HflC; Provisional; Region: PRK11029 187272001778 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 187272001779 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 187272001780 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 187272001781 dimer interface [polypeptide binding]; other site 187272001782 motif 1; other site 187272001783 active site 187272001784 motif 2; other site 187272001785 motif 3; other site 187272001786 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 187272001787 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 187272001788 GDP-binding site [chemical binding]; other site 187272001789 ACT binding site; other site 187272001790 IMP binding site; other site 187272001791 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 187272001792 ribonuclease R; Region: RNase_R; TIGR02063 187272001793 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 187272001794 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 187272001795 RNB domain; Region: RNB; pfam00773 187272001796 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 187272001797 RNA binding site [nucleotide binding]; other site 187272001798 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 187272001799 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 187272001800 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 187272001801 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 187272001802 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 187272001803 generic binding surface II; other site 187272001804 generic binding surface I; other site 187272001805 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 187272001806 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 187272001807 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 187272001808 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 187272001809 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 187272001810 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 187272001811 Walker A motif; other site 187272001812 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 187272001813 protein-splicing catalytic site; other site 187272001814 thioester formation/cholesterol transfer; other site 187272001815 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 187272001816 non-specific DNA binding site [nucleotide binding]; other site 187272001817 salt bridge; other site 187272001818 sequence-specific DNA binding site [nucleotide binding]; other site 187272001819 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 187272001820 protein-splicing catalytic site; other site 187272001821 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 187272001822 Walker B motif; other site 187272001823 DNA binding loops [nucleotide binding] 187272001824 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 187272001825 protein-splicing catalytic site; other site 187272001826 thioester formation/cholesterol transfer; other site 187272001827 Intein/homing endonuclease [DNA replication, recombination, and repair]; Region: COG1372 187272001828 Hint (Hedgehog/Intein) domain C-terminal region; Region: HintC; smart00305 187272001829 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 187272001830 alanine racemase; Reviewed; Region: alr; PRK00053 187272001831 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 187272001832 active site 187272001833 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 187272001834 substrate binding site [chemical binding]; other site 187272001835 catalytic residues [active] 187272001836 dimer interface [polypeptide binding]; other site 187272001837 DNA repair protein RadA; Provisional; Region: PRK11823 187272001838 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 187272001839 Walker A motif/ATP binding site; other site 187272001840 ATP binding site [chemical binding]; other site 187272001841 Walker B motif; other site 187272001842 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 187272001843 PilZ domain; Region: PilZ; cl01260 187272001844 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 187272001845 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 187272001846 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 187272001847 homodimer interface [polypeptide binding]; other site 187272001848 NADP binding site [chemical binding]; other site 187272001849 substrate binding site [chemical binding]; other site 187272001850 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 187272001851 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 187272001852 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 187272001853 trimer interface [polypeptide binding]; other site 187272001854 eyelet of channel; other site 187272001855 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 187272001856 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 187272001857 trimer interface [polypeptide binding]; other site 187272001858 eyelet of channel; other site 187272001859 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 187272001860 putative GSH binding site [chemical binding]; other site 187272001861 catalytic residues [active] 187272001862 GTP-binding protein Der; Reviewed; Region: PRK00093 187272001863 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 187272001864 G1 box; other site 187272001865 GTP/Mg2+ binding site [chemical binding]; other site 187272001866 Switch I region; other site 187272001867 G2 box; other site 187272001868 Switch II region; other site 187272001869 G3 box; other site 187272001870 G4 box; other site 187272001871 G5 box; other site 187272001872 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 187272001873 G1 box; other site 187272001874 GTP/Mg2+ binding site [chemical binding]; other site 187272001875 Switch I region; other site 187272001876 G2 box; other site 187272001877 G3 box; other site 187272001878 Switch II region; other site 187272001879 G4 box; other site 187272001880 G5 box; other site 187272001881 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 187272001882 active site 187272001883 substrate binding pocket [chemical binding]; other site 187272001884 dimer interface [polypeptide binding]; other site 187272001885 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 187272001886 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 187272001887 putative active site [active] 187272001888 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 187272001889 putative active site [active] 187272001890 Uncharacterized conserved protein [Function unknown]; Region: COG3189 187272001891 Hemerythrin-like domain; Region: Hr-like; cd12108 187272001892 Fe binding site [ion binding]; other site 187272001893 argininosuccinate synthase; Provisional; Region: PRK13820 187272001894 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 187272001895 ANP binding site [chemical binding]; other site 187272001896 Substrate Binding Site II [chemical binding]; other site 187272001897 Substrate Binding Site I [chemical binding]; other site 187272001898 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 187272001899 Flavoprotein; Region: Flavoprotein; pfam02441 187272001900 aromatic acid decarboxylase; Validated; Region: PRK05920 187272001901 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 187272001902 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 187272001903 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272001904 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 187272001905 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 187272001906 dimer interface [polypeptide binding]; other site 187272001907 substrate binding site [chemical binding]; other site 187272001908 metal binding sites [ion binding]; metal-binding site 187272001909 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 187272001910 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 187272001911 S-adenosylmethionine binding site [chemical binding]; other site 187272001912 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 187272001913 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 187272001914 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 187272001915 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 187272001916 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 187272001917 purine monophosphate binding site [chemical binding]; other site 187272001918 dimer interface [polypeptide binding]; other site 187272001919 putative catalytic residues [active] 187272001920 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 187272001921 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 187272001922 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 187272001923 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 187272001924 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 187272001925 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 187272001926 Phasin protein; Region: Phasin_2; cl11491 187272001927 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 187272001928 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 187272001929 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 187272001930 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 187272001931 Peptidase family M23; Region: Peptidase_M23; pfam01551 187272001932 ABC transporter ATPase component; Reviewed; Region: PRK11147 187272001933 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272001934 Walker A/P-loop; other site 187272001935 ATP binding site [chemical binding]; other site 187272001936 Q-loop/lid; other site 187272001937 ABC transporter signature motif; other site 187272001938 Walker B; other site 187272001939 D-loop; other site 187272001940 H-loop/switch region; other site 187272001941 ABC transporter; Region: ABC_tran_2; pfam12848 187272001942 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272001943 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 187272001944 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 187272001945 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 187272001946 S-adenosylmethionine binding site [chemical binding]; other site 187272001947 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 187272001948 Predicted permeases [General function prediction only]; Region: COG0679 187272001949 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 187272001950 dimerization interface [polypeptide binding]; other site 187272001951 putative DNA binding site [nucleotide binding]; other site 187272001952 putative Zn2+ binding site [ion binding]; other site 187272001953 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272001954 active site residue [active] 187272001955 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 187272001956 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 187272001957 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 187272001958 catalytic residue [active] 187272001959 DsrE/DsrF-like family; Region: DrsE; cl00672 187272001960 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 187272001961 S-adenosylmethionine binding site [chemical binding]; other site 187272001962 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 187272001963 Sodium Bile acid symporter family; Region: SBF; cl17470 187272001964 circadian clock protein KaiC; Reviewed; Region: PRK09302 187272001965 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 187272001966 ATP binding site [chemical binding]; other site 187272001967 Walker B motif; other site 187272001968 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 187272001969 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 187272001970 Walker A motif; other site 187272001971 Walker A motif; other site 187272001972 ATP binding site [chemical binding]; other site 187272001973 Walker B motif; other site 187272001974 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272001975 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272001976 active site 187272001977 I-site; other site 187272001978 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 187272001979 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 187272001980 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 187272001981 ligand binding site [chemical binding]; other site 187272001982 flexible hinge region; other site 187272001983 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 187272001984 putative switch regulator; other site 187272001985 non-specific DNA interactions [nucleotide binding]; other site 187272001986 DNA binding site [nucleotide binding] 187272001987 sequence specific DNA binding site [nucleotide binding]; other site 187272001988 putative cAMP binding site [chemical binding]; other site 187272001989 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 187272001990 thiosulfate reductase PhsA; Provisional; Region: PRK15488 187272001991 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 187272001992 molybdopterin cofactor binding site; other site 187272001993 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 187272001994 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 187272001995 putative molybdopterin cofactor binding site; other site 187272001996 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 187272001997 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 187272001998 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 187272001999 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 187272002000 Predicted permeases [General function prediction only]; Region: COG0679 187272002001 integrase; Provisional; Region: PRK09692 187272002002 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 187272002003 active site 187272002004 Int/Topo IB signature motif; other site 187272002005 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 187272002006 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 187272002007 Terminase-like family; Region: Terminase_6; pfam03237 187272002008 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 187272002009 Phage capsid family; Region: Phage_capsid; pfam05065 187272002010 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 187272002011 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272002012 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 187272002013 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 187272002014 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 187272002015 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 187272002016 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 187272002017 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 187272002018 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 187272002019 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272002020 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272002021 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272002022 Cation transport protein; Region: TrkH; cl17365 187272002023 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 187272002024 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 187272002025 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 187272002026 ligand binding site; other site 187272002027 oligomer interface; other site 187272002028 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 187272002029 dimer interface [polypeptide binding]; other site 187272002030 N-terminal domain interface [polypeptide binding]; other site 187272002031 sulfate 1 binding site; other site 187272002032 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 187272002033 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 187272002034 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 187272002035 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 187272002036 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 187272002037 Soluble P-type ATPase [General function prediction only]; Region: COG4087 187272002038 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 187272002039 potassium/proton antiporter; Reviewed; Region: PRK05326 187272002040 Transporter associated domain; Region: CorC_HlyC; smart01091 187272002041 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 187272002042 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 187272002043 FOG: CBS domain [General function prediction only]; Region: COG0517 187272002044 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_17; cd04630 187272002045 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 187272002046 S-adenosylmethionine binding site [chemical binding]; other site 187272002047 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 187272002048 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 187272002049 inhibitor-cofactor binding pocket; inhibition site 187272002050 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272002051 catalytic residue [active] 187272002052 tartrate dehydrogenase; Provisional; Region: PRK08194 187272002053 isocitrate dehydrogenase; Provisional; Region: PRK08997 187272002054 PAS domain S-box; Region: sensory_box; TIGR00229 187272002055 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 187272002056 putative active site [active] 187272002057 heme pocket [chemical binding]; other site 187272002058 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272002059 GAF domain; Region: GAF; pfam01590 187272002060 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 187272002061 PAS domain; Region: PAS_9; pfam13426 187272002062 putative active site [active] 187272002063 heme pocket [chemical binding]; other site 187272002064 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002065 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002066 metal binding site [ion binding]; metal-binding site 187272002067 active site 187272002068 I-site; other site 187272002069 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 187272002070 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 187272002071 Na binding site [ion binding]; other site 187272002072 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 187272002073 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 187272002074 dimer interface [polypeptide binding]; other site 187272002075 phosphorylation site [posttranslational modification] 187272002076 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272002077 ATP binding site [chemical binding]; other site 187272002078 Mg2+ binding site [ion binding]; other site 187272002079 G-X-G motif; other site 187272002080 PAS domain; Region: PAS; smart00091 187272002081 PAS domain; Region: PAS_9; pfam13426 187272002082 putative active site [active] 187272002083 heme pocket [chemical binding]; other site 187272002084 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 187272002085 active site 187272002086 catalytic site [active] 187272002087 substrate binding site [chemical binding]; other site 187272002088 Response regulator receiver domain; Region: Response_reg; pfam00072 187272002089 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272002090 active site 187272002091 phosphorylation site [posttranslational modification] 187272002092 intermolecular recognition site; other site 187272002093 dimerization interface [polypeptide binding]; other site 187272002094 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 187272002095 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 187272002096 ligand binding site [chemical binding]; other site 187272002097 flexible hinge region; other site 187272002098 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272002099 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272002100 metal binding triad; other site 187272002101 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 187272002102 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 187272002103 binding surface 187272002104 TPR motif; other site 187272002105 TPR repeat; Region: TPR_11; pfam13414 187272002106 acetyl-CoA synthetase; Provisional; Region: PRK00174 187272002107 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 187272002108 active site 187272002109 CoA binding site [chemical binding]; other site 187272002110 acyl-activating enzyme (AAE) consensus motif; other site 187272002111 AMP binding site [chemical binding]; other site 187272002112 acetate binding site [chemical binding]; other site 187272002113 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272002114 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272002115 active site 187272002116 phosphorylation site [posttranslational modification] 187272002117 intermolecular recognition site; other site 187272002118 dimerization interface [polypeptide binding]; other site 187272002119 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 187272002120 Walker A motif; other site 187272002121 ATP binding site [chemical binding]; other site 187272002122 Walker B motif; other site 187272002123 arginine finger; other site 187272002124 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 187272002125 Na binding site [ion binding]; other site 187272002126 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 187272002127 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 187272002128 putative active site [active] 187272002129 heme pocket [chemical binding]; other site 187272002130 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 187272002131 dimer interface [polypeptide binding]; other site 187272002132 phosphorylation site [posttranslational modification] 187272002133 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272002134 ATP binding site [chemical binding]; other site 187272002135 Mg2+ binding site [ion binding]; other site 187272002136 G-X-G motif; other site 187272002137 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 187272002138 active site 187272002139 HIGH motif; other site 187272002140 nucleotide binding site [chemical binding]; other site 187272002141 KMSKS motif; other site 187272002142 Protein required for attachment to host cells; Region: Host_attach; pfam10116 187272002143 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 187272002144 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 187272002145 Walker A/P-loop; other site 187272002146 ATP binding site [chemical binding]; other site 187272002147 Q-loop/lid; other site 187272002148 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 187272002149 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 187272002150 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 187272002151 ABC transporter signature motif; other site 187272002152 Walker B; other site 187272002153 D-loop; other site 187272002154 H-loop/switch region; other site 187272002155 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 187272002156 FtsZ protein binding site [polypeptide binding]; other site 187272002157 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 187272002158 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 187272002159 nucleotide binding pocket [chemical binding]; other site 187272002160 K-X-D-G motif; other site 187272002161 catalytic site [active] 187272002162 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 187272002163 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 187272002164 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 187272002165 DNA binding site [nucleotide binding] 187272002166 metal binding site [ion binding]; metal-binding site 187272002167 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 187272002168 Dimer interface [polypeptide binding]; other site 187272002169 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 187272002170 PAS domain S-box; Region: sensory_box; TIGR00229 187272002171 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002172 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002173 metal binding site [ion binding]; metal-binding site 187272002174 active site 187272002175 I-site; other site 187272002176 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 187272002177 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 187272002178 Radical SAM superfamily; Region: Radical_SAM; pfam04055 187272002179 FeS/SAM binding site; other site 187272002180 elongation factor P; Validated; Region: PRK00529 187272002181 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 187272002182 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 187272002183 RNA binding site [nucleotide binding]; other site 187272002184 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 187272002185 RNA binding site [nucleotide binding]; other site 187272002186 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 187272002187 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 187272002188 motif 1; other site 187272002189 dimer interface [polypeptide binding]; other site 187272002190 active site 187272002191 motif 2; other site 187272002192 motif 3; other site 187272002193 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 187272002194 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 187272002195 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 187272002196 active site 187272002197 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 187272002198 beta-ketothiolase; Provisional; Region: PRK09051 187272002199 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 187272002200 dimer interface [polypeptide binding]; other site 187272002201 active site 187272002202 Response regulator receiver domain; Region: Response_reg; pfam00072 187272002203 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272002204 active site 187272002205 phosphorylation site [posttranslational modification] 187272002206 intermolecular recognition site; other site 187272002207 dimerization interface [polypeptide binding]; other site 187272002208 PAS domain S-box; Region: sensory_box; TIGR00229 187272002209 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 187272002210 putative active site [active] 187272002211 heme pocket [chemical binding]; other site 187272002212 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002213 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002214 metal binding site [ion binding]; metal-binding site 187272002215 active site 187272002216 I-site; other site 187272002217 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 187272002218 HDOD domain; Region: HDOD; pfam08668 187272002219 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cd09680 187272002220 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 187272002221 dimer interface [polypeptide binding]; other site 187272002222 HAMP domain; Region: HAMP; pfam00672 187272002223 dimerization interface [polypeptide binding]; other site 187272002224 PAS domain S-box; Region: sensory_box; TIGR00229 187272002225 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 187272002226 putative active site [active] 187272002227 heme pocket [chemical binding]; other site 187272002228 PAS domain S-box; Region: sensory_box; TIGR00229 187272002229 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 187272002230 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002231 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002232 metal binding site [ion binding]; metal-binding site 187272002233 active site 187272002234 I-site; other site 187272002235 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 187272002236 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 187272002237 generic binding surface II; other site 187272002238 generic binding surface I; other site 187272002239 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 187272002240 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 187272002241 diiron binding motif [ion binding]; other site 187272002242 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11866 187272002243 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 187272002244 TPP-binding site [chemical binding]; other site 187272002245 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 187272002246 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 187272002247 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 187272002248 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 187272002249 dimer interface [polypeptide binding]; other site 187272002250 PYR/PP interface [polypeptide binding]; other site 187272002251 TPP binding site [chemical binding]; other site 187272002252 substrate binding site [chemical binding]; other site 187272002253 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 187272002254 flagellin; Provisional; Region: PRK12806 187272002255 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 187272002256 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 187272002257 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 187272002258 TPR motif; other site 187272002259 binding surface 187272002260 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 187272002261 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 187272002262 flagellin; Provisional; Region: PRK12806 187272002263 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 187272002264 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 187272002265 FlaG protein; Region: FlaG; pfam03646 187272002266 FlaG protein; Region: FlaG; pfam03646 187272002267 flagellar capping protein; Reviewed; Region: fliD; PRK08032 187272002268 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 187272002269 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 187272002270 flagellar protein FliS; Validated; Region: fliS; PRK05685 187272002271 transcriptional regulatory protein ZraR; Provisional; Region: PRK10365 187272002272 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 187272002273 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 187272002274 Walker A motif; other site 187272002275 ATP binding site [chemical binding]; other site 187272002276 Walker B motif; other site 187272002277 arginine finger; other site 187272002278 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272002279 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272002280 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 187272002281 Walker A motif; other site 187272002282 ATP binding site [chemical binding]; other site 187272002283 Walker B motif; other site 187272002284 arginine finger; other site 187272002285 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272002286 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 187272002287 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 187272002288 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 187272002289 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 187272002290 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 187272002291 MgtE intracellular N domain; Region: MgtE_N; cl15244 187272002292 FliG C-terminal domain; Region: FliG_C; pfam01706 187272002293 flagellar assembly protein H; Validated; Region: fliH; PRK05687 187272002294 Flagellar assembly protein FliH; Region: FliH; pfam02108 187272002295 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 187272002296 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 187272002297 Walker A motif/ATP binding site; other site 187272002298 Walker B motif; other site 187272002299 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 187272002300 Flagellar FliJ protein; Region: FliJ; pfam02050 187272002301 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 187272002302 heat shock protein HtpX; Provisional; Region: PRK05457 187272002303 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 187272002304 EamA-like transporter family; Region: EamA; pfam00892 187272002305 EamA-like transporter family; Region: EamA; pfam00892 187272002306 BolA-like protein; Region: BolA; pfam01722 187272002307 YciI-like protein; Reviewed; Region: PRK11370 187272002308 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 187272002309 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 187272002310 active site 187272002311 HIGH motif; other site 187272002312 dimer interface [polypeptide binding]; other site 187272002313 KMSKS motif; other site 187272002314 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272002315 active site 187272002316 KMSKS motif; other site 187272002317 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 187272002318 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 187272002319 FeS assembly SUF system regulator, gammaproteobacterial; Region: suf_reg_Xantho; TIGR02944 187272002320 Transcriptional regulator; Region: Rrf2; pfam02082 187272002321 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 187272002322 putative ABC transporter; Region: ycf24; CHL00085 187272002323 FeS assembly ATPase SufC; Region: sufC; TIGR01978 187272002324 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 187272002325 Walker A/P-loop; other site 187272002326 ATP binding site [chemical binding]; other site 187272002327 Q-loop/lid; other site 187272002328 ABC transporter signature motif; other site 187272002329 Walker B; other site 187272002330 D-loop; other site 187272002331 H-loop/switch region; other site 187272002332 FeS assembly protein SufD; Region: sufD; TIGR01981 187272002333 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 187272002334 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 187272002335 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 187272002336 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 187272002337 catalytic residue [active] 187272002338 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 187272002339 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 187272002340 trimerization site [polypeptide binding]; other site 187272002341 active site 187272002342 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272002343 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 187272002344 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272002345 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272002346 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 187272002347 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 187272002348 Walker A/P-loop; other site 187272002349 ATP binding site [chemical binding]; other site 187272002350 Q-loop/lid; other site 187272002351 ABC transporter signature motif; other site 187272002352 Walker B; other site 187272002353 D-loop; other site 187272002354 H-loop/switch region; other site 187272002355 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 187272002356 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 187272002357 dimer interface [polypeptide binding]; other site 187272002358 conserved gate region; other site 187272002359 putative PBP binding loops; other site 187272002360 ABC-ATPase subunit interface; other site 187272002361 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 187272002362 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 187272002363 Domain of unknown function (DUF4382); Region: DUF4382; pfam14321 187272002364 Ferrochelatase; Region: Ferrochelatase; pfam00762 187272002365 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 187272002366 C-terminal domain interface [polypeptide binding]; other site 187272002367 active site 187272002368 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 187272002369 active site 187272002370 N-terminal domain interface [polypeptide binding]; other site 187272002371 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 187272002372 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 187272002373 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 187272002374 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 187272002375 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 187272002376 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272002377 hydrogenase 4 subunit F; Validated; Region: PRK06458 187272002378 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272002379 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 187272002380 nudix motif; other site 187272002381 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 187272002382 quinolinate synthetase; Provisional; Region: PRK09375 187272002383 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 187272002384 Major Facilitator Superfamily; Region: MFS_1; pfam07690 187272002385 putative substrate translocation pore; other site 187272002386 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 187272002387 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 187272002388 NAD-dependent deacetylase; Provisional; Region: PRK05333 187272002389 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 187272002390 radical SAM/Cys-rich domain protein; Region: rSAM_SeCys; TIGR04167 187272002391 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 187272002392 FeS/SAM binding site; other site 187272002393 Protein of unknown function (DUF3641); Region: DUF3641; pfam12345 187272002394 mercuric reductase; Validated; Region: PRK06370 187272002395 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272002396 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272002397 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272002398 Uncharacterized conserved protein [Function unknown]; Region: COG0398 187272002399 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 187272002400 transferase 1, rSAM/selenodomain-associated; Region: glyco_like_cofC; TIGR04282 187272002401 GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function; Region: GT_2_like_a; cd02522 187272002402 transferase 2, rSAM/selenodomain-associated; Region: glyco_like_mftF; TIGR04283 187272002403 Probable Catalytic site; other site 187272002404 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 187272002405 dimerization interface [polypeptide binding]; other site 187272002406 putative DNA binding site [nucleotide binding]; other site 187272002407 putative Zn2+ binding site [ion binding]; other site 187272002408 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272002409 active site residue [active] 187272002410 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 187272002411 Rubredoxin; Region: Rubredoxin; pfam00301 187272002412 iron binding site [ion binding]; other site 187272002413 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 187272002414 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272002415 CHASE domain; Region: CHASE; cl01369 187272002416 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 187272002417 PAS domain; Region: PAS_9; pfam13426 187272002418 putative active site [active] 187272002419 heme pocket [chemical binding]; other site 187272002420 PAS fold; Region: PAS_4; pfam08448 187272002421 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002422 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002423 metal binding site [ion binding]; metal-binding site 187272002424 active site 187272002425 I-site; other site 187272002426 MASE1; Region: MASE1; cl17823 187272002427 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002428 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002429 metal binding site [ion binding]; metal-binding site 187272002430 active site 187272002431 I-site; other site 187272002432 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 187272002433 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 187272002434 DNA binding residues [nucleotide binding] 187272002435 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 187272002436 IHF dimer interface [polypeptide binding]; other site 187272002437 IHF - DNA interface [nucleotide binding]; other site 187272002438 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 187272002439 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 187272002440 putative tRNA-binding site [nucleotide binding]; other site 187272002441 B3/4 domain; Region: B3_4; pfam03483 187272002442 tRNA synthetase B5 domain; Region: B5; smart00874 187272002443 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 187272002444 dimer interface [polypeptide binding]; other site 187272002445 motif 1; other site 187272002446 motif 3; other site 187272002447 motif 2; other site 187272002448 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 187272002449 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 187272002450 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 187272002451 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 187272002452 dimer interface [polypeptide binding]; other site 187272002453 motif 1; other site 187272002454 active site 187272002455 motif 2; other site 187272002456 motif 3; other site 187272002457 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 187272002458 23S rRNA binding site [nucleotide binding]; other site 187272002459 L21 binding site [polypeptide binding]; other site 187272002460 L13 binding site [polypeptide binding]; other site 187272002461 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 187272002462 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 187272002463 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 187272002464 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 187272002465 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 187272002466 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 187272002467 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 187272002468 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 187272002469 active site 187272002470 dimer interface [polypeptide binding]; other site 187272002471 motif 1; other site 187272002472 motif 2; other site 187272002473 motif 3; other site 187272002474 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 187272002475 anticodon binding site; other site 187272002476 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 187272002477 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 187272002478 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 187272002479 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 187272002480 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 187272002481 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 187272002482 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 187272002483 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 187272002484 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 187272002485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 187272002486 Uncharacterized conserved protein [Function unknown]; Region: COG2308 187272002487 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 187272002488 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 187272002489 Spore Coat Protein U domain; Region: SCPU; pfam05229 187272002490 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 187272002491 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 187272002492 PapC C-terminal domain; Region: PapC_C; pfam13953 187272002493 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 187272002494 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 187272002495 Spore Coat Protein U domain; Region: SCPU; pfam05229 187272002496 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 187272002497 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 187272002498 N-terminal plug; other site 187272002499 ligand-binding site [chemical binding]; other site 187272002500 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 187272002501 4Fe-4S binding domain; Region: Fer4_5; pfam12801 187272002502 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 187272002503 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 187272002504 benzoyl-CoA reductase, subunit C; Region: benz_CoA_red_C; TIGR02263 187272002505 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 187272002506 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 187272002507 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 187272002508 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 187272002509 TPP-binding site [chemical binding]; other site 187272002510 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 187272002511 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 187272002512 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 187272002513 dimer interface [polypeptide binding]; other site 187272002514 PYR/PP interface [polypeptide binding]; other site 187272002515 TPP binding site [chemical binding]; other site 187272002516 substrate binding site [chemical binding]; other site 187272002517 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 187272002518 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 187272002519 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 187272002520 active site 187272002521 catalytic residues [active] 187272002522 DNA binding site [nucleotide binding] 187272002523 Int/Topo IB signature motif; other site 187272002524 Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the...; Region: Prim_Pol; cd04859 187272002525 polymerase nucleotide-binding site; other site 187272002526 DNA-binding residues [nucleotide binding]; DNA binding site 187272002527 nucleotide binding site [chemical binding]; other site 187272002528 primase nucleotide-binding site [nucleotide binding]; other site 187272002529 Primase C terminal 1 (PriCT-1); Region: PriCT_1; smart00942 187272002530 AAA domain; Region: AAA_25; pfam13481 187272002531 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 187272002532 ATP binding site [chemical binding]; other site 187272002533 Walker A motif; other site 187272002534 Walker B motif; other site 187272002535 Terminase-like family; Region: Terminase_6; pfam03237 187272002536 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 187272002537 Phage capsid family; Region: Phage_capsid; pfam05065 187272002538 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 187272002539 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 187272002540 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 187272002541 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 187272002542 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 187272002543 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 187272002544 Low molecular weight phosphatase family; Region: LMWPc; cd00115 187272002545 active site 187272002546 polysaccharide export protein Wza; Provisional; Region: PRK15078 187272002547 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 187272002548 SLBB domain; Region: SLBB; pfam10531 187272002549 tyrosine kinase; Provisional; Region: PRK11519 187272002550 Chain length determinant protein; Region: Wzz; pfam02706 187272002551 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 187272002552 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 187272002553 P-loop; other site 187272002554 Magnesium ion binding site [ion binding]; other site 187272002555 transport-energizing ATPase, TRC40/GET3/ArsA family; Region: GET3_arsA_TRC40; TIGR00345 187272002556 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 187272002557 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 187272002558 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 187272002559 NAD(P) binding site [chemical binding]; other site 187272002560 homodimer interface [polypeptide binding]; other site 187272002561 substrate binding site [chemical binding]; other site 187272002562 active site 187272002563 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 187272002564 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 187272002565 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 187272002566 NAD(P) binding site [chemical binding]; other site 187272002567 homodimer interface [polypeptide binding]; other site 187272002568 substrate binding site [chemical binding]; other site 187272002569 active site 187272002570 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 187272002571 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 187272002572 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 187272002573 Family description; Region: UvrD_C_2; pfam13538 187272002574 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 187272002575 AAA domain; Region: AAA_30; pfam13604 187272002576 Family description; Region: UvrD_C_2; pfam13538 187272002577 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 187272002578 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 187272002579 inhibitor-cofactor binding pocket; inhibition site 187272002580 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272002581 catalytic residue [active] 187272002582 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 187272002583 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 187272002584 LssY C-terminus; Region: LssY_C; pfam14067 187272002585 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 187272002586 endonuclease III; Provisional; Region: PRK10702 187272002587 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 187272002588 minor groove reading motif; other site 187272002589 helix-hairpin-helix signature motif; other site 187272002590 substrate binding pocket [chemical binding]; other site 187272002591 active site 187272002592 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 187272002593 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 187272002594 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 187272002595 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 187272002596 motif II; other site 187272002597 electron transport complex RsxE subunit; Provisional; Region: PRK12405 187272002598 FMN-binding domain; Region: FMN_bind; cl01081 187272002599 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 187272002600 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 187272002601 SLBB domain; Region: SLBB; pfam10531 187272002602 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 187272002603 ferredoxin; Provisional; Region: PRK08764 187272002604 4Fe-4S binding domain; Region: Fer4; pfam00037 187272002605 electron transport complex protein RsxA; Provisional; Region: PRK05151 187272002606 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 187272002607 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 187272002608 active site 187272002609 HIGH motif; other site 187272002610 KMSKS motif; other site 187272002611 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 187272002612 tRNA binding surface [nucleotide binding]; other site 187272002613 anticodon binding site; other site 187272002614 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 187272002615 dimer interface [polypeptide binding]; other site 187272002616 putative tRNA-binding site [nucleotide binding]; other site 187272002617 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 187272002618 CrcB-like protein; Region: CRCB; pfam02537 187272002619 Peptidase family M48; Region: Peptidase_M48; cl12018 187272002620 Bacitracin resistance protein BacA; Region: BacA; pfam02673 187272002621 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 187272002622 trimer interface [polypeptide binding]; other site 187272002623 eyelet of channel; other site 187272002624 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 187272002625 MgtE intracellular N domain; Region: MgtE_N; pfam03448 187272002626 FOG: CBS domain [General function prediction only]; Region: COG0517 187272002627 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272002628 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 187272002629 MgtE intracellular N domain; Region: MgtE_N; smart00924 187272002630 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 187272002631 Divalent cation transporter; Region: MgtE; pfam01769 187272002632 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 187272002633 trimer interface [polypeptide binding]; other site 187272002634 active site 187272002635 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 187272002636 ArsC family; Region: ArsC; pfam03960 187272002637 catalytic residues [active] 187272002638 AAA domain; Region: AAA_23; pfam13476 187272002639 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272002640 Walker A/P-loop; other site 187272002641 ATP binding site [chemical binding]; other site 187272002642 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272002643 ABC transporter signature motif; other site 187272002644 Walker B; other site 187272002645 D-loop; other site 187272002646 H-loop/switch region; other site 187272002647 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 187272002648 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 187272002649 active site 187272002650 metal binding site [ion binding]; metal-binding site 187272002651 DNA binding site [nucleotide binding] 187272002652 peroxiredoxin; Provisional; Region: PRK13189 187272002653 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 187272002654 dimer interface [polypeptide binding]; other site 187272002655 decamer (pentamer of dimers) interface [polypeptide binding]; other site 187272002656 catalytic triad [active] 187272002657 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 187272002658 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 187272002659 active site 187272002660 PAS fold; Region: PAS_4; pfam08448 187272002661 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 187272002662 putative active site [active] 187272002663 heme pocket [chemical binding]; other site 187272002664 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 187272002665 PAS domain; Region: PAS_9; pfam13426 187272002666 putative active site [active] 187272002667 heme pocket [chemical binding]; other site 187272002668 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272002669 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272002670 metal binding site [ion binding]; metal-binding site 187272002671 active site 187272002672 I-site; other site 187272002673 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 187272002674 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 187272002675 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 187272002676 substrate binding pocket [chemical binding]; other site 187272002677 chain length determination region; other site 187272002678 substrate-Mg2+ binding site; other site 187272002679 catalytic residues [active] 187272002680 aspartate-rich region 1; other site 187272002681 active site lid residues [active] 187272002682 aspartate-rich region 2; other site 187272002683 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 187272002684 Ligand Binding Site [chemical binding]; other site 187272002685 BCCT family transporter; Region: BCCT; pfam02028 187272002686 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 187272002687 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 187272002688 active site 187272002689 catalytic site [active] 187272002690 substrate binding site [chemical binding]; other site 187272002691 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 187272002692 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 187272002693 ligand binding site [chemical binding]; other site 187272002694 flexible hinge region; other site 187272002695 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 187272002696 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272002697 metal binding triad; other site 187272002698 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 187272002699 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 187272002700 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 187272002701 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 187272002702 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 187272002703 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 187272002704 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 187272002705 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 187272002706 Obg family GTPase CgtA; Region: Obg_CgtA; TIGR02729 187272002707 GTP1/OBG; Region: GTP1_OBG; pfam01018 187272002708 Obg GTPase; Region: Obg; cd01898 187272002709 G1 box; other site 187272002710 GTP/Mg2+ binding site [chemical binding]; other site 187272002711 Switch I region; other site 187272002712 G2 box; other site 187272002713 G3 box; other site 187272002714 Switch II region; other site 187272002715 G4 box; other site 187272002716 G5 box; other site 187272002717 gamma-glutamyl kinase; Provisional; Region: PRK05429 187272002718 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 187272002719 nucleotide binding site [chemical binding]; other site 187272002720 homotetrameric interface [polypeptide binding]; other site 187272002721 putative phosphate binding site [ion binding]; other site 187272002722 putative allosteric binding site; other site 187272002723 PUA domain; Region: PUA; pfam01472 187272002724 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 187272002725 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 187272002726 MviN-like protein; Region: MVIN; pfam03023 187272002727 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 187272002728 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 187272002729 active site 187272002730 Riboflavin kinase; Region: Flavokinase; smart00904 187272002731 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 187272002732 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272002733 active site 187272002734 HIGH motif; other site 187272002735 nucleotide binding site [chemical binding]; other site 187272002736 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 187272002737 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 187272002738 active site 187272002739 KMSKS motif; other site 187272002740 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 187272002741 tRNA binding surface [nucleotide binding]; other site 187272002742 anticodon binding site; other site 187272002743 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 187272002744 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 187272002745 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 187272002746 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 187272002747 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 187272002748 Type II transport protein GspH; Region: GspH; pfam12019 187272002749 Type II transport protein GspH; Region: GspH; pfam12019 187272002750 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 187272002751 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 187272002752 PilX N-terminal; Region: PilX_N; pfam14341 187272002753 PilX N-terminal; Region: PilX_N; pfam14341 187272002754 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 187272002755 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 187272002756 active site 187272002757 NTP binding site [chemical binding]; other site 187272002758 metal binding triad [ion binding]; metal-binding site 187272002759 antibiotic binding site [chemical binding]; other site 187272002760 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 187272002761 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 187272002762 Cu(I) binding site [ion binding]; other site 187272002763 HemK family putative methylases; Region: hemK_fam; TIGR00536 187272002764 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 187272002765 S-adenosylmethionine binding site [chemical binding]; other site 187272002766 Peptidase family M48; Region: Peptidase_M48; pfam01435 187272002767 TPR repeat; Region: TPR_11; pfam13414 187272002768 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 187272002769 TPR motif; other site 187272002770 binding surface 187272002771 TPR repeat; Region: TPR_11; pfam13414 187272002772 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 187272002773 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 187272002774 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 187272002775 ATP binding site [chemical binding]; other site 187272002776 putative Mg++ binding site [ion binding]; other site 187272002777 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 187272002778 nucleotide binding region [chemical binding]; other site 187272002779 ATP-binding site [chemical binding]; other site 187272002780 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 187272002781 HRDC domain; Region: HRDC; pfam00570 187272002782 Predicted permeases [General function prediction only]; Region: COG0679 187272002783 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 187272002784 DctM-like transporters; Region: DctM; pfam06808 187272002785 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 187272002786 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 187272002787 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 187272002788 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 187272002789 tetramerization interface [polypeptide binding]; other site 187272002790 NAD(P) binding site [chemical binding]; other site 187272002791 catalytic residues [active] 187272002792 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 187272002793 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; Region: 2-Hacid_dh; pfam00389 187272002794 NAD binding site [chemical binding]; other site 187272002795 ligand binding site [chemical binding]; other site 187272002796 catalytic site [active] 187272002797 aspartate aminotransferase; Provisional; Region: PRK05764 187272002798 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 187272002799 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272002800 homodimer interface [polypeptide binding]; other site 187272002801 catalytic residue [active] 187272002802 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 187272002803 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 187272002804 N-terminal plug; other site 187272002805 ligand-binding site [chemical binding]; other site 187272002806 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 187272002807 CoenzymeA binding site [chemical binding]; other site 187272002808 subunit interaction site [polypeptide binding]; other site 187272002809 PHB binding site; other site 187272002810 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 187272002811 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 187272002812 CoenzymeA binding site [chemical binding]; other site 187272002813 subunit interaction site [polypeptide binding]; other site 187272002814 PHB binding site; other site 187272002815 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 187272002816 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272002817 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272002818 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 187272002819 lipoyl-biotinyl attachment site [posttranslational modification]; other site 187272002820 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272002821 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 187272002822 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 187272002823 RimM N-terminal domain; Region: RimM; pfam01782 187272002824 PRC-barrel domain; Region: PRC; pfam05239 187272002825 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 187272002826 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 187272002827 FlgN protein; Region: FlgN; pfam05130 187272002828 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 187272002829 SAF-like; Region: SAF_2; pfam13144 187272002830 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 187272002831 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 187272002832 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 187272002833 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272002834 active site 187272002835 phosphorylation site [posttranslational modification] 187272002836 intermolecular recognition site; other site 187272002837 dimerization interface [polypeptide binding]; other site 187272002838 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 187272002839 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 187272002840 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 187272002841 S-adenosylmethionine binding site [chemical binding]; other site 187272002842 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 187272002843 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 187272002844 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 187272002845 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 187272002846 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 187272002847 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 187272002848 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 187272002849 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 187272002850 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 187272002851 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 187272002852 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 187272002853 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 187272002854 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 187272002855 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 187272002856 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 187272002857 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 187272002858 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 187272002859 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 187272002860 Flagellar L-ring protein; Region: FlgH; pfam02107 187272002861 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 187272002862 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 187272002863 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 187272002864 Rod binding protein; Region: Rod-binding; cl01626 187272002865 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 187272002866 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 187272002867 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 187272002868 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 187272002869 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 187272002870 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 187272002871 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 187272002872 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 187272002873 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 187272002874 minor groove reading motif; other site 187272002875 helix-hairpin-helix signature motif; other site 187272002876 substrate binding pocket [chemical binding]; other site 187272002877 active site 187272002878 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 187272002879 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 187272002880 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 187272002881 NAD(P) binding site [chemical binding]; other site 187272002882 active site 187272002883 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 187272002884 substrate binding pocket [chemical binding]; other site 187272002885 substrate-Mg2+ binding site; other site 187272002886 aspartate-rich region 1; other site 187272002887 aspartate-rich region 2; other site 187272002888 ATP-grasp domain; Region: ATP-grasp_4; cl17255 187272002889 Predicted acyl esterases [General function prediction only]; Region: COG2936 187272002890 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; smart00939 187272002891 phosphoglycolate phosphatase; Provisional; Region: PRK13222 187272002892 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 187272002893 motif II; other site 187272002894 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 187272002895 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 187272002896 S-adenosylmethionine binding site [chemical binding]; other site 187272002897 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 187272002898 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 187272002899 active site 187272002900 putative substrate binding pocket [chemical binding]; other site 187272002901 shikimate kinase; Reviewed; Region: aroK; PRK00131 187272002902 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 187272002903 ADP binding site [chemical binding]; other site 187272002904 magnesium binding site [ion binding]; other site 187272002905 putative shikimate binding site; other site 187272002906 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 187272002907 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 187272002908 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 187272002909 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272002910 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272002911 OmpW family; Region: OmpW; cl17427 187272002912 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 187272002913 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 187272002914 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 187272002915 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 187272002916 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 187272002917 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 187272002918 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 187272002919 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 187272002920 potassium/proton antiporter; Reviewed; Region: PRK05326 187272002921 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 187272002922 TrkA-C domain; Region: TrkA_C; pfam02080 187272002923 Transporter associated domain; Region: CorC_HlyC; smart01091 187272002924 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 187272002925 substrate binding site [chemical binding]; other site 187272002926 DNA gyrase subunit A; Validated; Region: PRK05560 187272002927 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 187272002928 CAP-like domain; other site 187272002929 active site 187272002930 primary dimer interface [polypeptide binding]; other site 187272002931 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002932 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002933 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002934 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002935 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002936 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 187272002937 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 187272002938 homodimer interface [polypeptide binding]; other site 187272002939 substrate-cofactor binding pocket; other site 187272002940 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272002941 catalytic residue [active] 187272002942 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 187272002943 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 187272002944 putative ligand binding site [chemical binding]; other site 187272002945 putative NAD binding site [chemical binding]; other site 187272002946 putative catalytic site [active] 187272002947 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 187272002948 L-serine binding site [chemical binding]; other site 187272002949 ACT domain interface; other site 187272002950 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 187272002951 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 187272002952 Prephenate dehydratase; Region: PDT; pfam00800 187272002953 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 187272002954 putative L-Phe binding site [chemical binding]; other site 187272002955 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 187272002956 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 187272002957 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272002958 homodimer interface [polypeptide binding]; other site 187272002959 catalytic residue [active] 187272002960 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 187272002961 prephenate dehydrogenase; Validated; Region: PRK08507 187272002962 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 187272002963 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 187272002964 hinge; other site 187272002965 active site 187272002966 cytidylate kinase; Provisional; Region: cmk; PRK00023 187272002967 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 187272002968 CMP-binding site; other site 187272002969 The sites determining sugar specificity; other site 187272002970 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 187272002971 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 187272002972 RNA binding site [nucleotide binding]; other site 187272002973 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 187272002974 RNA binding site [nucleotide binding]; other site 187272002975 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 187272002976 RNA binding site [nucleotide binding]; other site 187272002977 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 187272002978 RNA binding site [nucleotide binding]; other site 187272002979 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 187272002980 RNA binding site [nucleotide binding]; other site 187272002981 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 187272002982 RNA binding site [nucleotide binding]; other site 187272002983 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 187272002984 IHF dimer interface [polypeptide binding]; other site 187272002985 IHF - DNA interface [nucleotide binding]; other site 187272002986 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 187272002987 tetratricopeptide repeat protein; Provisional; Region: PRK11788 187272002988 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 187272002989 binding surface 187272002990 TPR motif; other site 187272002991 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 187272002992 binding surface 187272002993 TPR motif; other site 187272002994 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 187272002995 binding surface 187272002996 TPR motif; other site 187272002997 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 187272002998 active site 187272002999 dimer interface [polypeptide binding]; other site 187272003000 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 187272003001 serine/threonine protein kinase; Provisional; Region: PRK11768 187272003002 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 187272003003 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 187272003004 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 187272003005 Cation efflux family; Region: Cation_efflux; cl00316 187272003006 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 187272003007 metal binding site 2 [ion binding]; metal-binding site 187272003008 putative DNA binding helix; other site 187272003009 metal binding site 1 [ion binding]; metal-binding site 187272003010 dimer interface [polypeptide binding]; other site 187272003011 structural Zn2+ binding site [ion binding]; other site 187272003012 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3492 187272003013 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 187272003014 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 187272003015 G1 box; other site 187272003016 putative GEF interaction site [polypeptide binding]; other site 187272003017 GTP/Mg2+ binding site [chemical binding]; other site 187272003018 Switch I region; other site 187272003019 G2 box; other site 187272003020 G3 box; other site 187272003021 Switch II region; other site 187272003022 G4 box; other site 187272003023 G5 box; other site 187272003024 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 187272003025 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 187272003026 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 187272003027 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 187272003028 Ligand Binding Site [chemical binding]; other site 187272003029 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 187272003030 putative GTP cyclohydrolase; Provisional; Region: PRK13674 187272003031 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 187272003032 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 187272003033 substrate binding pocket [chemical binding]; other site 187272003034 chain length determination region; other site 187272003035 substrate-Mg2+ binding site; other site 187272003036 catalytic residues [active] 187272003037 aspartate-rich region 1; other site 187272003038 active site lid residues [active] 187272003039 aspartate-rich region 2; other site 187272003040 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 187272003041 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 187272003042 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003043 Mg2+ binding site [ion binding]; other site 187272003044 G-X-G motif; other site 187272003045 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 187272003046 anchoring element; other site 187272003047 dimer interface [polypeptide binding]; other site 187272003048 ATP binding site [chemical binding]; other site 187272003049 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 187272003050 active site 187272003051 putative metal-binding site [ion binding]; other site 187272003052 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 187272003053 CRISPR-associated protein (Cas_Cas2CT1978); Region: Cas_Cas2CT1978; pfam09707 187272003054 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 187272003055 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 187272003056 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-E; cd09645 187272003057 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-E; cl09608 187272003058 CRISPR/Cas system-associated protein Cse2; Region: Cse2_I-E; cd09731 187272003059 CRISPR/Cas system-associated protein Cse1; Region: Cse1_I-E; cl08044 187272003060 helicase Cas3; Provisional; Region: PRK09694 187272003061 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 187272003062 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 187272003063 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 187272003064 This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important...; Region: GT1_Glycogen_Phosphorylase_like; cd04299 187272003065 putative homodimer interface [polypeptide binding]; other site 187272003066 putative active site pocket [active] 187272003067 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 187272003068 glycogen synthase; Provisional; Region: glgA; PRK00654 187272003069 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 187272003070 ADP-binding pocket [chemical binding]; other site 187272003071 homodimer interface [polypeptide binding]; other site 187272003072 glycogen branching enzyme; Provisional; Region: PRK05402 187272003073 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 187272003074 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 187272003075 active site 187272003076 catalytic site [active] 187272003077 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 187272003078 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 187272003079 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 187272003080 ligand binding site; other site 187272003081 oligomer interface; other site 187272003082 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 187272003083 dimer interface [polypeptide binding]; other site 187272003084 N-terminal domain interface [polypeptide binding]; other site 187272003085 sulfate 1 binding site; other site 187272003086 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 187272003087 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 187272003088 putative active site [active] 187272003089 catalytic site [active] 187272003090 4-alpha-glucanotransferase; Provisional; Region: PRK14508 187272003091 Predicted integral membrane protein [Function unknown]; Region: COG5615 187272003092 Dinitrogenase iron-molybdenum cofactor; Region: Nitro_FeMo-Co; pfam02579 187272003093 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 187272003094 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 187272003095 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 187272003096 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 187272003097 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272003098 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 187272003099 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 187272003100 CAP-like domain; other site 187272003101 active site 187272003102 primary dimer interface [polypeptide binding]; other site 187272003103 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4619 187272003104 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272003105 Walker A/P-loop; other site 187272003106 ATP binding site [chemical binding]; other site 187272003107 Q-loop/lid; other site 187272003108 ABC transporter signature motif; other site 187272003109 Walker B; other site 187272003110 D-loop; other site 187272003111 H-loop/switch region; other site 187272003112 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 187272003113 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 187272003114 intersubunit interface [polypeptide binding]; other site 187272003115 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 187272003116 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 187272003117 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 187272003118 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 187272003119 flagellar motor switch protein; Validated; Region: fliN; PRK05698 187272003120 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 187272003121 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 187272003122 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 187272003123 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 187272003124 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 187272003125 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 187272003126 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 187272003127 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 187272003128 FHIPEP family; Region: FHIPEP; pfam00771 187272003129 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 187272003130 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 187272003131 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 187272003132 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 187272003133 P-loop; other site 187272003134 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 187272003135 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 187272003136 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 187272003137 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 187272003138 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 187272003139 DNA binding residues [nucleotide binding] 187272003140 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 187272003141 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272003142 active site 187272003143 phosphorylation site [posttranslational modification] 187272003144 intermolecular recognition site; other site 187272003145 dimerization interface [polypeptide binding]; other site 187272003146 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 187272003147 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 187272003148 putative binding surface; other site 187272003149 active site 187272003150 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 187272003151 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 187272003152 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003153 ATP binding site [chemical binding]; other site 187272003154 Mg2+ binding site [ion binding]; other site 187272003155 G-X-G motif; other site 187272003156 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 187272003157 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 187272003158 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272003159 active site 187272003160 phosphorylation site [posttranslational modification] 187272003161 intermolecular recognition site; other site 187272003162 dimerization interface [polypeptide binding]; other site 187272003163 CheB methylesterase; Region: CheB_methylest; pfam01339 187272003164 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 187272003165 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 187272003166 P-loop; other site 187272003167 Magnesium ion binding site [ion binding]; other site 187272003168 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 187272003169 Magnesium ion binding site [ion binding]; other site 187272003170 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 187272003171 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 187272003172 putative CheA interaction surface; other site 187272003173 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 187272003174 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 187272003175 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 187272003176 NAD(P) binding site [chemical binding]; other site 187272003177 homotetramer interface [polypeptide binding]; other site 187272003178 homodimer interface [polypeptide binding]; other site 187272003179 active site 187272003180 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 187272003181 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 187272003182 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 187272003183 DsrC like protein; Region: DsrC; pfam04358 187272003184 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 187272003185 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 187272003186 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 187272003187 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 187272003188 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 187272003189 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 187272003190 [4Fe-4S] binding site [ion binding]; other site 187272003191 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 187272003192 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 187272003193 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 187272003194 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 187272003195 molybdopterin cofactor binding site; other site 187272003196 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 187272003197 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 187272003198 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 187272003199 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 187272003200 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 187272003201 dimerization interface [polypeptide binding]; other site 187272003202 Histidine kinase; Region: HisKA_3; pfam07730 187272003203 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003204 ATP binding site [chemical binding]; other site 187272003205 Mg2+ binding site [ion binding]; other site 187272003206 G-X-G motif; other site 187272003207 transcriptional regulator NarL; Provisional; Region: PRK10651 187272003208 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272003209 active site 187272003210 phosphorylation site [posttranslational modification] 187272003211 intermolecular recognition site; other site 187272003212 dimerization interface [polypeptide binding]; other site 187272003213 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 187272003214 DNA binding residues [nucleotide binding] 187272003215 dimerization interface [polypeptide binding]; other site 187272003216 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 187272003217 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 187272003218 putative substrate translocation pore; other site 187272003219 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 187272003220 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 187272003221 Ligand Binding Site [chemical binding]; other site 187272003222 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 187272003223 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 187272003224 substrate binding pocket [chemical binding]; other site 187272003225 membrane-bound complex binding site; other site 187272003226 hinge residues; other site 187272003227 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 187272003228 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003229 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003230 metal binding site [ion binding]; metal-binding site 187272003231 active site 187272003232 I-site; other site 187272003233 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 187272003234 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 187272003235 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 187272003236 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 187272003237 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 187272003238 active site 187272003239 VIT family; Region: VIT1; pfam01988 187272003240 GMP synthase; Reviewed; Region: guaA; PRK00074 187272003241 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 187272003242 AMP/PPi binding site [chemical binding]; other site 187272003243 candidate oxyanion hole; other site 187272003244 catalytic triad [active] 187272003245 potential glutamine specificity residues [chemical binding]; other site 187272003246 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 187272003247 ATP Binding subdomain [chemical binding]; other site 187272003248 Ligand Binding sites [chemical binding]; other site 187272003249 Dimerization subdomain; other site 187272003250 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 187272003251 nucleoside/Zn binding site; other site 187272003252 dimer interface [polypeptide binding]; other site 187272003253 catalytic motif [active] 187272003254 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 187272003255 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 187272003256 substrate binding pocket [chemical binding]; other site 187272003257 membrane-bound complex binding site; other site 187272003258 hinge residues; other site 187272003259 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 187272003260 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272003261 catalytic residue [active] 187272003262 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 187272003263 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 187272003264 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 187272003265 active site 187272003266 Zn binding site [ion binding]; other site 187272003267 Protein of unknown function (DUF454); Region: DUF454; cl01063 187272003268 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 187272003269 Domain of unknown function (DUF1726); Region: DUF1726; pfam08351 187272003270 Helicase; Region: Helicase_RecD; pfam05127 187272003271 GNAT acetyltransferase 2; Region: GNAT_acetyltr_2; pfam13718 187272003272 Possible tRNA binding domain; Region: tRNA_bind_2; pfam13725 187272003273 Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit [Energy production and conversion / Inorganic ion transport and metabolism]; Region: HyfB; COG0651 187272003274 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272003275 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 187272003276 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 187272003277 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 187272003278 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 187272003279 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 187272003280 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 187272003281 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 187272003282 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 187272003283 motif II; other site 187272003284 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 187272003285 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 187272003286 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 187272003287 catalytic residues [active] 187272003288 Predicted membrane protein (DUF2319); Region: DUF2319; pfam10081 187272003289 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 187272003290 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 187272003291 Walker A motif; other site 187272003292 ATP binding site [chemical binding]; other site 187272003293 Walker B motif; other site 187272003294 arginine finger; other site 187272003295 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272003296 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 187272003297 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 187272003298 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 187272003299 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 187272003300 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 187272003301 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 187272003302 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 187272003303 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 187272003304 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 187272003305 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 187272003306 Peptidase M15; Region: Peptidase_M15_3; cl01194 187272003307 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 187272003308 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 187272003309 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 187272003310 Ligand Binding Site [chemical binding]; other site 187272003311 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 187272003312 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 187272003313 CoA binding domain; Region: CoA_binding_2; pfam13380 187272003314 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 187272003315 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 187272003316 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 187272003317 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272003318 Coenzyme A binding pocket [chemical binding]; other site 187272003319 GIY-YIG domain of hypothetical proteins from archaea and their bacterial homologs; Region: GIY-YIG_COG1833; cd10441 187272003320 GIY-YIG motif/motif A; other site 187272003321 putative active site [active] 187272003322 putative metal binding site [ion binding]; other site 187272003323 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 187272003324 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 187272003325 N-terminal plug; other site 187272003326 ligand-binding site [chemical binding]; other site 187272003327 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 187272003328 dimer interface [polypeptide binding]; other site 187272003329 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 187272003330 active site 187272003331 metal binding site [ion binding]; metal-binding site 187272003332 glutathione binding site [chemical binding]; other site 187272003333 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 187272003334 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 187272003335 intersubunit interface [polypeptide binding]; other site 187272003336 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 187272003337 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 187272003338 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 187272003339 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 187272003340 ABC-ATPase subunit interface; other site 187272003341 dimer interface [polypeptide binding]; other site 187272003342 putative PBP binding regions; other site 187272003343 Uncharacterized conserved protein [Function unknown]; Region: COG0397 187272003344 hypothetical protein; Validated; Region: PRK00029 187272003345 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 187272003346 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 187272003347 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272003348 catalytic residue [active] 187272003349 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 187272003350 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 187272003351 Surface antigen; Region: Bac_surface_Ag; pfam01103 187272003352 CHAT domain; Region: CHAT; pfam12770 187272003353 PrpA and PrpB, metallophosphatase domain; Region: MPP_PrpA_PrpB; cd07424 187272003354 active site 187272003355 metal binding site [ion binding]; metal-binding site 187272003356 SnoaL-like domain; Region: SnoaL_3; pfam13474 187272003357 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003358 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003359 metal binding site [ion binding]; metal-binding site 187272003360 active site 187272003361 I-site; other site 187272003362 HDOD domain; Region: HDOD; pfam08668 187272003363 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003364 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003365 metal binding site [ion binding]; metal-binding site 187272003366 active site 187272003367 I-site; other site 187272003368 DsrE/DsrF-like family; Region: DrsE; pfam02635 187272003369 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 187272003370 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272003371 Protein export membrane protein; Region: SecD_SecF; cl14618 187272003372 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272003373 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272003374 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272003375 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272003376 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 187272003377 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 187272003378 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 187272003379 FAD binding pocket [chemical binding]; other site 187272003380 FAD binding motif [chemical binding]; other site 187272003381 phosphate binding motif [ion binding]; other site 187272003382 beta-alpha-beta structure motif; other site 187272003383 NAD binding pocket [chemical binding]; other site 187272003384 Iron coordination center [ion binding]; other site 187272003385 integrase; Provisional; Region: PRK09692 187272003386 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 187272003387 active site 187272003388 DNA binding site [nucleotide binding] 187272003389 Int/Topo IB signature motif; other site 187272003390 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 187272003391 large terminase protein; Provisional; Region: 17; PHA02533 187272003392 Terminase-like family; Region: Terminase_6; pfam03237 187272003393 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 187272003394 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 187272003395 ligand binding site [chemical binding]; other site 187272003396 flexible hinge region; other site 187272003397 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 187272003398 putative switch regulator; other site 187272003399 non-specific DNA interactions [nucleotide binding]; other site 187272003400 DNA binding site [nucleotide binding] 187272003401 sequence specific DNA binding site [nucleotide binding]; other site 187272003402 putative cAMP binding site [chemical binding]; other site 187272003403 Cytochrome c553 [Energy production and conversion]; Region: COG2863 187272003404 Cytochrome c553 [Energy production and conversion]; Region: COG2863 187272003405 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 187272003406 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 187272003407 4Fe-4S binding domain; Region: Fer4_5; pfam12801 187272003408 nitrous-oxide reductase; Validated; Region: PRK02888 187272003409 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 187272003410 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 187272003411 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 187272003412 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 187272003413 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 187272003414 Walker A/P-loop; other site 187272003415 ATP binding site [chemical binding]; other site 187272003416 Q-loop/lid; other site 187272003417 ABC transporter signature motif; other site 187272003418 Walker B; other site 187272003419 D-loop; other site 187272003420 H-loop/switch region; other site 187272003421 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 187272003422 NosL; Region: NosL; pfam05573 187272003423 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 187272003424 putative hydrolase; Provisional; Region: PRK11460 187272003425 NosL; Region: NosL; pfam05573 187272003426 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 187272003427 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 187272003428 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272003429 Walker A/P-loop; other site 187272003430 ATP binding site [chemical binding]; other site 187272003431 Q-loop/lid; other site 187272003432 ABC transporter signature motif; other site 187272003433 Walker B; other site 187272003434 D-loop; other site 187272003435 H-loop/switch region; other site 187272003436 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 187272003437 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 187272003438 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272003439 Walker A/P-loop; other site 187272003440 ATP binding site [chemical binding]; other site 187272003441 Q-loop/lid; other site 187272003442 ABC transporter signature motif; other site 187272003443 Walker B; other site 187272003444 D-loop; other site 187272003445 H-loop/switch region; other site 187272003446 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 187272003447 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 187272003448 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 187272003449 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 187272003450 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 187272003451 dimer interface [polypeptide binding]; other site 187272003452 conserved gate region; other site 187272003453 putative PBP binding loops; other site 187272003454 ABC-ATPase subunit interface; other site 187272003455 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 187272003456 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 187272003457 aspartate aminotransferase; Provisional; Region: PRK05764 187272003458 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 187272003459 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272003460 homodimer interface [polypeptide binding]; other site 187272003461 catalytic residue [active] 187272003462 excinuclease ABC subunit B; Provisional; Region: PRK05298 187272003463 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 187272003464 ATP binding site [chemical binding]; other site 187272003465 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 187272003466 nucleotide binding region [chemical binding]; other site 187272003467 ATP-binding site [chemical binding]; other site 187272003468 Ultra-violet resistance protein B; Region: UvrB; pfam12344 187272003469 UvrB/uvrC motif; Region: UVR; pfam02151 187272003470 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 187272003471 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 187272003472 RNA binding surface [nucleotide binding]; other site 187272003473 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 187272003474 probable active site [active] 187272003475 Nitrate and nitrite sensing; Region: NIT; pfam08376 187272003476 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003477 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003478 metal binding site [ion binding]; metal-binding site 187272003479 active site 187272003480 I-site; other site 187272003481 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 187272003482 nodulation ABC transporter NodI; Provisional; Region: PRK13537 187272003483 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272003484 Walker A/P-loop; other site 187272003485 ATP binding site [chemical binding]; other site 187272003486 Q-loop/lid; other site 187272003487 ABC transporter signature motif; other site 187272003488 Walker B; other site 187272003489 D-loop; other site 187272003490 H-loop/switch region; other site 187272003491 ABC-2 type transporter; Region: ABC2_membrane; cl17235 187272003492 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 187272003493 DNA Polymerase Y-family; Region: PolY_like; cd03468 187272003494 DNA binding site [nucleotide binding] 187272003495 Uncharacterized conserved protein [Function unknown]; Region: COG4544 187272003496 LexA repressor; Validated; Region: PRK00215 187272003497 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 187272003498 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 187272003499 Catalytic site [active] 187272003500 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 187272003501 HD domain; Region: HD_4; pfam13328 187272003502 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 187272003503 synthetase active site [active] 187272003504 NTP binding site [chemical binding]; other site 187272003505 metal binding site [ion binding]; metal-binding site 187272003506 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 187272003507 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 187272003508 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 187272003509 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 187272003510 dimerization interface [polypeptide binding]; other site 187272003511 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 187272003512 dimer interface [polypeptide binding]; other site 187272003513 putative CheW interface [polypeptide binding]; other site 187272003514 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 187272003515 PAS domain; Region: PAS_9; pfam13426 187272003516 putative active site [active] 187272003517 heme pocket [chemical binding]; other site 187272003518 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 187272003519 PAS fold; Region: PAS_3; pfam08447 187272003520 putative active site [active] 187272003521 heme pocket [chemical binding]; other site 187272003522 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003523 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003524 metal binding site [ion binding]; metal-binding site 187272003525 active site 187272003526 I-site; other site 187272003527 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 187272003528 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 187272003529 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 187272003530 Walker A/P-loop; other site 187272003531 ATP binding site [chemical binding]; other site 187272003532 Q-loop/lid; other site 187272003533 ABC transporter signature motif; other site 187272003534 Walker B; other site 187272003535 D-loop; other site 187272003536 H-loop/switch region; other site 187272003537 TOBE domain; Region: TOBE_2; pfam08402 187272003538 ornithine carbamoyltransferase; Provisional; Region: PRK00779 187272003539 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 187272003540 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 187272003541 acetylornithine aminotransferase; Provisional; Region: PRK02627 187272003542 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 187272003543 inhibitor-cofactor binding pocket; inhibition site 187272003544 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272003545 catalytic residue [active] 187272003546 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 187272003547 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 187272003548 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 187272003549 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 187272003550 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 187272003551 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 187272003552 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272003553 active site 187272003554 phosphorylation site [posttranslational modification] 187272003555 intermolecular recognition site; other site 187272003556 dimerization interface [polypeptide binding]; other site 187272003557 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 187272003558 DNA binding site [nucleotide binding] 187272003559 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 187272003560 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 187272003561 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 187272003562 putative active site [active] 187272003563 heme pocket [chemical binding]; other site 187272003564 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 187272003565 dimer interface [polypeptide binding]; other site 187272003566 phosphorylation site [posttranslational modification] 187272003567 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003568 ATP binding site [chemical binding]; other site 187272003569 Mg2+ binding site [ion binding]; other site 187272003570 G-X-G motif; other site 187272003571 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 187272003572 PAS domain; Region: PAS_9; pfam13426 187272003573 putative active site [active] 187272003574 heme pocket [chemical binding]; other site 187272003575 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003576 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003577 metal binding site [ion binding]; metal-binding site 187272003578 active site 187272003579 I-site; other site 187272003580 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 187272003581 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3973 187272003582 Part of AAA domain; Region: AAA_19; pfam13245 187272003583 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 187272003584 Family description; Region: UvrD_C_2; pfam13538 187272003585 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 187272003586 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 187272003587 putative active site [active] 187272003588 heme pocket [chemical binding]; other site 187272003589 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003590 ATP binding site [chemical binding]; other site 187272003591 Mg2+ binding site [ion binding]; other site 187272003592 G-X-G motif; other site 187272003593 PBP superfamily domain; Region: PBP_like_2; cl17296 187272003594 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 187272003595 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 187272003596 trimer interface [polypeptide binding]; other site 187272003597 eyelet of channel; other site 187272003598 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 187272003599 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 187272003600 ligand binding site [chemical binding]; other site 187272003601 flexible hinge region; other site 187272003602 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 187272003603 non-specific DNA interactions [nucleotide binding]; other site 187272003604 DNA binding site [nucleotide binding] 187272003605 sequence specific DNA binding site [nucleotide binding]; other site 187272003606 putative cAMP binding site [chemical binding]; other site 187272003607 PAS fold; Region: PAS; pfam00989 187272003608 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 187272003609 putative active site [active] 187272003610 heme pocket [chemical binding]; other site 187272003611 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003612 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003613 metal binding site [ion binding]; metal-binding site 187272003614 active site 187272003615 I-site; other site 187272003616 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 187272003617 PAS domain; Region: PAS_9; pfam13426 187272003618 putative active site [active] 187272003619 heme pocket [chemical binding]; other site 187272003620 CheB methylesterase; Region: CheB_methylest; pfam01339 187272003621 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 187272003622 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 187272003623 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 187272003624 PAS domain; Region: PAS_10; pfam13596 187272003625 BON domain; Region: BON; cl02771 187272003626 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 187272003627 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 187272003628 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 187272003629 Fic/DOC family; Region: Fic; pfam02661 187272003630 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 187272003631 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 187272003632 Walker A motif; other site 187272003633 ATP binding site [chemical binding]; other site 187272003634 Walker B motif; other site 187272003635 arginine finger; other site 187272003636 Uncharacterized conserved protein [Function unknown]; Region: COG3410 187272003637 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 187272003638 Catalytic site [active] 187272003639 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 187272003640 homodimer interface [polypeptide binding]; other site 187272003641 chemical substrate binding site [chemical binding]; other site 187272003642 oligomer interface [polypeptide binding]; other site 187272003643 metal binding site [ion binding]; metal-binding site 187272003644 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 187272003645 OsmC-like protein; Region: OsmC; pfam02566 187272003646 Transposase [DNA replication, recombination, and repair]; Region: COG5421 187272003647 Nuclease-related domain; Region: NERD; pfam08378 187272003648 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272003649 Sel1-like repeats; Region: SEL1; smart00671 187272003650 Sel1 repeat; Region: Sel1; cl02723 187272003651 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 187272003652 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 187272003653 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 187272003654 dimer interface [polypeptide binding]; other site 187272003655 conserved gate region; other site 187272003656 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 187272003657 dimer interface [polypeptide binding]; other site 187272003658 ABC-ATPase subunit interface; other site 187272003659 conserved gate region; other site 187272003660 putative PBP binding loops; other site 187272003661 ABC-ATPase subunit interface; other site 187272003662 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 187272003663 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 187272003664 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 187272003665 dimer interface [polypeptide binding]; other site 187272003666 conserved gate region; other site 187272003667 putative PBP binding loops; other site 187272003668 ABC-ATPase subunit interface; other site 187272003669 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 187272003670 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 187272003671 Walker A/P-loop; other site 187272003672 ATP binding site [chemical binding]; other site 187272003673 Q-loop/lid; other site 187272003674 ABC transporter signature motif; other site 187272003675 Walker B; other site 187272003676 D-loop; other site 187272003677 H-loop/switch region; other site 187272003678 transcriptional regulator PhoU; Provisional; Region: PRK11115 187272003679 PhoU domain; Region: PhoU; pfam01895 187272003680 PhoU domain; Region: PhoU; pfam01895 187272003681 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272003682 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272003683 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 187272003684 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 187272003685 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 187272003686 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 187272003687 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 187272003688 Yip1 domain; Region: Yip1; pfam04893 187272003689 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 187272003690 osmolarity response regulator; Provisional; Region: ompR; PRK09468 187272003691 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272003692 active site 187272003693 phosphorylation site [posttranslational modification] 187272003694 intermolecular recognition site; other site 187272003695 dimerization interface [polypeptide binding]; other site 187272003696 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 187272003697 DNA binding site [nucleotide binding] 187272003698 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 187272003699 dimerization interface [polypeptide binding]; other site 187272003700 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 187272003701 dimer interface [polypeptide binding]; other site 187272003702 phosphorylation site [posttranslational modification] 187272003703 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272003704 ATP binding site [chemical binding]; other site 187272003705 Mg2+ binding site [ion binding]; other site 187272003706 G-X-G motif; other site 187272003707 Bacterial PH domain; Region: DUF304; cl01348 187272003708 Bacterial PH domain; Region: DUF304; pfam03703 187272003709 Bacterial PH domain; Region: DUF304; cl01348 187272003710 Bacterial PH domain; Region: DUF304; pfam03703 187272003711 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 187272003712 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 187272003713 dimer interface [polypeptide binding]; other site 187272003714 putative CheW interface [polypeptide binding]; other site 187272003715 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 187272003716 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 187272003717 dimer interface [polypeptide binding]; other site 187272003718 putative CheW interface [polypeptide binding]; other site 187272003719 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 187272003720 Transglycosylase; Region: Transgly; pfam00912 187272003721 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 187272003722 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 187272003723 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 187272003724 DEAD/DEAH box helicase; Region: DEAD; pfam00270 187272003725 DEAD_2; Region: DEAD_2; pfam06733 187272003726 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 187272003727 Domain of unknown function (DUF1992); Region: DUF1992; cl08096 187272003728 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 187272003729 VPS10 domain; Region: VPS10; smart00602 187272003730 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 187272003731 MPN+ (JAMM) motif; other site 187272003732 Zinc-binding site [ion binding]; other site 187272003733 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 187272003734 MoaE interaction surface [polypeptide binding]; other site 187272003735 MoeB interaction surface [polypeptide binding]; other site 187272003736 thiocarboxylated glycine; other site 187272003737 molybdopterin biosynthesis protein MoeB; Validated; Region: PRK08762 187272003738 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272003739 active site residue [active] 187272003740 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 187272003741 ATP binding site [chemical binding]; other site 187272003742 substrate interface [chemical binding]; other site 187272003743 Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; Region: DHR2_DOCK; cl06123 187272003744 Cytochrome c; Region: Cytochrom_C; pfam00034 187272003745 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 187272003746 Cytochrome C' Region: Cytochrom_C_2; pfam01322 187272003747 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 187272003748 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 187272003749 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 187272003750 Domain of unknown function DUF21; Region: DUF21; pfam01595 187272003751 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 187272003752 Transporter associated domain; Region: CorC_HlyC; smart01091 187272003753 Cupin domain; Region: Cupin_2; pfam07883 187272003754 Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; Region: RLP_RrRLP; cd08210 187272003755 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed; Region: mtnW; PRK09549 187272003756 dimer interface [polypeptide binding]; other site 187272003757 active site 187272003758 catalytic residue [active] 187272003759 metal binding site [ion binding]; metal-binding site 187272003760 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 187272003761 EamA-like transporter family; Region: EamA; pfam00892 187272003762 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272003763 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272003764 metal binding site [ion binding]; metal-binding site 187272003765 active site 187272003766 I-site; other site 187272003767 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 187272003768 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 187272003769 RNA binding surface [nucleotide binding]; other site 187272003770 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 187272003771 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 187272003772 putative active site [active] 187272003773 putative PHP Thumb interface [polypeptide binding]; other site 187272003774 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 187272003775 generic binding surface II; other site 187272003776 generic binding surface I; other site 187272003777 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 187272003778 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 187272003779 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 187272003780 putative inner membrane protein; Provisional; Region: PRK11099 187272003781 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 187272003782 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 187272003783 active site residue [active] 187272003784 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 187272003785 active site residue [active] 187272003786 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 187272003787 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272003788 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272003789 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272003790 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 187272003791 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 187272003792 ligand binding site [chemical binding]; other site 187272003793 flexible hinge region; other site 187272003794 Domain of unknown function DUF77; Region: DUF77; pfam01910 187272003795 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 187272003796 FeS/SAM binding site; other site 187272003797 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272003798 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 187272003799 E3 interaction surface; other site 187272003800 lipoyl attachment site [posttranslational modification]; other site 187272003801 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272003802 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272003803 Protein export membrane protein; Region: SecD_SecF; cl14618 187272003804 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 187272003805 generic binding surface II; other site 187272003806 generic binding surface I; other site 187272003807 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 187272003808 putative active site [active] 187272003809 putative catalytic site [active] 187272003810 putative Mg binding site IVb [ion binding]; other site 187272003811 putative phosphate binding site [ion binding]; other site 187272003812 putative DNA binding site [nucleotide binding]; other site 187272003813 putative Mg binding site IVa [ion binding]; other site 187272003814 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; pfam09982 187272003815 L-ectoine synthase; Reviewed; Region: ectC; PRK13290 187272003816 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 187272003817 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 187272003818 inhibitor-cofactor binding pocket; inhibition site 187272003819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272003820 catalytic residue [active] 187272003821 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 187272003822 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272003823 Coenzyme A binding pocket [chemical binding]; other site 187272003824 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 187272003825 Glycoprotease family; Region: Peptidase_M22; pfam00814 187272003826 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 187272003827 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 187272003828 metal binding site [ion binding]; metal-binding site 187272003829 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 187272003830 metal binding site 2 [ion binding]; metal-binding site 187272003831 putative DNA binding helix; other site 187272003832 metal binding site 1 [ion binding]; metal-binding site 187272003833 dimer interface [polypeptide binding]; other site 187272003834 structural Zn2+ binding site [ion binding]; other site 187272003835 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 187272003836 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272003837 Walker A/P-loop; other site 187272003838 ATP binding site [chemical binding]; other site 187272003839 Q-loop/lid; other site 187272003840 ABC transporter signature motif; other site 187272003841 Walker B; other site 187272003842 D-loop; other site 187272003843 H-loop/switch region; other site 187272003844 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 187272003845 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 187272003846 ABC-ATPase subunit interface; other site 187272003847 dimer interface [polypeptide binding]; other site 187272003848 putative PBP binding regions; other site 187272003849 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 187272003850 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 187272003851 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 187272003852 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 187272003853 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272003854 Walker A/P-loop; other site 187272003855 ATP binding site [chemical binding]; other site 187272003856 Q-loop/lid; other site 187272003857 ABC transporter signature motif; other site 187272003858 Walker B; other site 187272003859 D-loop; other site 187272003860 H-loop/switch region; other site 187272003861 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 187272003862 Protein of unknown function (DUF330); Region: DUF330; cl01135 187272003863 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 187272003864 mce related protein; Region: MCE; pfam02470 187272003865 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 187272003866 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 187272003867 Walker A/P-loop; other site 187272003868 ATP binding site [chemical binding]; other site 187272003869 Q-loop/lid; other site 187272003870 ABC transporter signature motif; other site 187272003871 Walker B; other site 187272003872 D-loop; other site 187272003873 H-loop/switch region; other site 187272003874 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 187272003875 Permease; Region: Permease; pfam02405 187272003876 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 187272003877 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 187272003878 AAA domain; Region: AAA_33; pfam13671 187272003879 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 187272003880 active site 187272003881 glutamate--cysteine ligase; Region: PLN02611 187272003882 Protein of unknown function (DUF523); Region: DUF523; pfam04463 187272003883 Uncharacterized conserved protein [Function unknown]; Region: COG3272 187272003884 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 187272003885 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 187272003886 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 187272003887 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 187272003888 Protein export membrane protein; Region: SecD_SecF; cl14618 187272003889 Protein export membrane protein; Region: SecD_SecF; cl14618 187272003890 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 187272003891 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 187272003892 putative MPT binding site; other site 187272003893 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 187272003894 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 187272003895 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 187272003896 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 187272003897 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 187272003898 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 187272003899 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 187272003900 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 187272003901 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 187272003902 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 187272003903 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 187272003904 Protein export membrane protein; Region: SecD_SecF; pfam02355 187272003905 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 187272003906 FOG: CBS domain [General function prediction only]; Region: COG0517 187272003907 PrkA family serine protein kinase; Provisional; Region: PRK15455 187272003908 AAA ATPase domain; Region: AAA_16; pfam13191 187272003909 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 187272003910 hypothetical protein; Provisional; Region: PRK05325 187272003911 SpoVR family protein; Provisional; Region: PRK11767 187272003912 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 187272003913 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 187272003914 catalytic triad [active] 187272003915 dimer interface [polypeptide binding]; other site 187272003916 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 187272003917 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 187272003918 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272003919 Coenzyme A binding pocket [chemical binding]; other site 187272003920 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 187272003921 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 187272003922 Tetramer interface [polypeptide binding]; other site 187272003923 active site 187272003924 FMN-binding site [chemical binding]; other site 187272003925 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 187272003926 MFS_1 like family; Region: MFS_1_like; pfam12832 187272003927 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 187272003928 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 187272003929 substrate binding site [chemical binding]; other site 187272003930 ligand binding site [chemical binding]; other site 187272003931 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 187272003932 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 187272003933 substrate binding site [chemical binding]; other site 187272003934 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 187272003935 tartrate dehydrogenase; Provisional; Region: PRK08194 187272003936 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 187272003937 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 187272003938 FimV N-terminal domain; Region: FimV_core; TIGR03505 187272003939 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 187272003940 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 187272003941 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 187272003942 dimerization interface 3.5A [polypeptide binding]; other site 187272003943 active site 187272003944 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 187272003945 active site 187272003946 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 187272003947 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 187272003948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272003949 catalytic residue [active] 187272003950 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 187272003951 substrate binding site [chemical binding]; other site 187272003952 active site 187272003953 catalytic residues [active] 187272003954 heterodimer interface [polypeptide binding]; other site 187272003955 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 187272003956 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 187272003957 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 187272003958 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272003959 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; cl03649 187272003960 Sporulation related domain; Region: SPOR; pfam05036 187272003961 Colicin V production protein; Region: Colicin_V; pfam02674 187272003962 amidophosphoribosyltransferase; Provisional; Region: PRK09246 187272003963 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 187272003964 active site 187272003965 tetramer interface [polypeptide binding]; other site 187272003966 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272003967 active site 187272003968 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 187272003969 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 187272003970 homodimer interface [polypeptide binding]; other site 187272003971 substrate-cofactor binding pocket; other site 187272003972 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272003973 catalytic residue [active] 187272003974 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 187272003975 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 187272003976 active site 187272003977 dimerization interface [polypeptide binding]; other site 187272003978 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 187272003979 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 187272003980 serine O-acetyltransferase; Region: cysE; TIGR01172 187272003981 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 187272003982 trimer interface [polypeptide binding]; other site 187272003983 active site 187272003984 substrate binding site [chemical binding]; other site 187272003985 CoA binding site [chemical binding]; other site 187272003986 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 187272003987 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 187272003988 active site 187272003989 multimer interface [polypeptide binding]; other site 187272003990 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 187272003991 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 187272003992 FeS/SAM binding site; other site 187272003993 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 187272003994 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 187272003995 TPR motif; other site 187272003996 binding surface 187272003997 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 187272003998 binding surface 187272003999 TPR motif; other site 187272004000 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 187272004001 non-specific DNA binding site [nucleotide binding]; other site 187272004002 salt bridge; other site 187272004003 sequence-specific DNA binding site [nucleotide binding]; other site 187272004004 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 187272004005 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 187272004006 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 187272004007 dimer interface [polypeptide binding]; other site 187272004008 motif 1; other site 187272004009 active site 187272004010 motif 2; other site 187272004011 motif 3; other site 187272004012 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 187272004013 anticodon binding site; other site 187272004014 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 187272004015 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 187272004016 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 187272004017 Trp docking motif [polypeptide binding]; other site 187272004018 active site 187272004019 NRDE protein; Region: NRDE; cl01315 187272004020 adenylate kinase; Reviewed; Region: adk; PRK00279 187272004021 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 187272004022 AMP-binding site [chemical binding]; other site 187272004023 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 187272004024 Protein of unknown function (DUF2288); Region: DUF2288; pfam10052 187272004025 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 187272004026 catalytic triad [active] 187272004027 metal binding site [ion binding]; metal-binding site 187272004028 conserved cis-peptide bond; other site 187272004029 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 187272004030 putative active site pocket [active] 187272004031 dimerization interface [polypeptide binding]; other site 187272004032 putative catalytic residue [active] 187272004033 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 187272004034 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 187272004035 G1 box; other site 187272004036 putative GEF interaction site [polypeptide binding]; other site 187272004037 GTP/Mg2+ binding site [chemical binding]; other site 187272004038 Switch I region; other site 187272004039 G2 box; other site 187272004040 CysD dimerization site [polypeptide binding]; other site 187272004041 G3 box; other site 187272004042 Switch II region; other site 187272004043 G4 box; other site 187272004044 G5 box; other site 187272004045 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 187272004046 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 187272004047 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 187272004048 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 187272004049 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 187272004050 Active Sites [active] 187272004051 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 187272004052 active site 187272004053 SAM binding site [chemical binding]; other site 187272004054 homodimer interface [polypeptide binding]; other site 187272004055 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 187272004056 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 187272004057 Active Sites [active] 187272004058 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 187272004059 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 187272004060 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 187272004061 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 187272004062 Cytochrome c; Region: Cytochrom_C; cl11414 187272004063 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 187272004064 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272004065 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 187272004066 Predicted transporter component [General function prediction only]; Region: COG2391 187272004067 Sulphur transport; Region: Sulf_transp; pfam04143 187272004068 Predicted secreted protein [Function unknown]; Region: COG5501 187272004069 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 187272004070 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 187272004071 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 187272004072 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 187272004073 Predicted membrane protein [Function unknown]; Region: COG3235 187272004074 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 187272004075 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 187272004076 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1); Region: TDT_SLAC1_like; cd09323 187272004077 gating phenylalanine in ion channel; other site 187272004078 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 187272004079 Glutathione S-transferase, N-terminal domain; Region: GST_N_2; pfam13409 187272004080 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 187272004081 putative dimer interface [polypeptide binding]; other site 187272004082 N-terminal domain interface [polypeptide binding]; other site 187272004083 putative substrate binding pocket (H-site) [chemical binding]; other site 187272004084 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 187272004085 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 187272004086 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 187272004087 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 187272004088 dimer interface [polypeptide binding]; other site 187272004089 putative functional site; other site 187272004090 putative MPT binding site; other site 187272004091 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; cl17855 187272004092 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 187272004093 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 187272004094 FeS/SAM binding site; other site 187272004095 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 187272004096 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 187272004097 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 187272004098 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 187272004099 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 187272004100 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 187272004101 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 187272004102 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 187272004103 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 187272004104 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 187272004105 [4Fe-4S] binding site [ion binding]; other site 187272004106 molybdopterin cofactor binding site; other site 187272004107 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 187272004108 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 187272004109 molybdopterin cofactor binding site; other site 187272004110 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 187272004111 4Fe-4S binding domain; Region: Fer4; cl02805 187272004112 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 187272004113 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 187272004114 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 187272004115 Ubiquitin-like proteins; Region: UBQ; cl00155 187272004116 charged pocket; other site 187272004117 hydrophobic patch; other site 187272004118 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 187272004119 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272004120 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272004121 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272004122 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 187272004123 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 187272004124 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 187272004125 formate dehydrogenase-H ferredoxin subunit; Provisional; Region: PRK10330 187272004126 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 187272004127 homodecamer interface [polypeptide binding]; other site 187272004128 GTP cyclohydrolase I; Provisional; Region: PLN03044 187272004129 active site 187272004130 putative catalytic site residues [active] 187272004131 zinc binding site [ion binding]; other site 187272004132 GTP-CH-I/GFRP interaction surface; other site 187272004133 D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional; Region: folX; PRK11245 187272004134 active site 187272004135 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 187272004136 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 187272004137 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272004138 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272004139 metal binding site [ion binding]; metal-binding site 187272004140 active site 187272004141 I-site; other site 187272004142 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 187272004143 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 187272004144 HIGH motif; other site 187272004145 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 187272004146 active site 187272004147 KMSKS motif; other site 187272004148 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 187272004149 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 187272004150 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 187272004151 GTP binding site; other site 187272004152 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 187272004153 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 187272004154 dimerization interface [polypeptide binding]; other site 187272004155 putative DNA binding site [nucleotide binding]; other site 187272004156 putative Zn2+ binding site [ion binding]; other site 187272004157 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 187272004158 high affinity sulphate transporter 1; Region: sulP; TIGR00815 187272004159 Sulfate transporter family; Region: Sulfate_transp; pfam00916 187272004160 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 187272004161 methionine sulfoxide reductase A; Provisional; Region: PRK14054 187272004162 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 187272004163 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 187272004164 Walker A motif; other site 187272004165 ATP binding site [chemical binding]; other site 187272004166 Walker B motif; other site 187272004167 arginine finger; other site 187272004168 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272004169 Family description; Region: DsbD_2; pfam13386 187272004170 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 187272004171 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 187272004172 Walker A/P-loop; other site 187272004173 ATP binding site [chemical binding]; other site 187272004174 Q-loop/lid; other site 187272004175 ABC transporter signature motif; other site 187272004176 Walker B; other site 187272004177 D-loop; other site 187272004178 H-loop/switch region; other site 187272004179 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 187272004180 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 187272004181 universal stress protein UspE; Provisional; Region: PRK11175 187272004182 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 187272004183 Ligand Binding Site [chemical binding]; other site 187272004184 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 187272004185 Ligand Binding Site [chemical binding]; other site 187272004186 glycerol kinase; Provisional; Region: glpK; PRK00047 187272004187 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 187272004188 N- and C-terminal domain interface [polypeptide binding]; other site 187272004189 active site 187272004190 MgATP binding site [chemical binding]; other site 187272004191 catalytic site [active] 187272004192 metal binding site [ion binding]; metal-binding site 187272004193 glycerol binding site [chemical binding]; other site 187272004194 homotetramer interface [polypeptide binding]; other site 187272004195 homodimer interface [polypeptide binding]; other site 187272004196 FBP binding site [chemical binding]; other site 187272004197 protein IIAGlc interface [polypeptide binding]; other site 187272004198 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 187272004199 ThiC-associated domain; Region: ThiC-associated; pfam13667 187272004200 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 187272004201 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 187272004202 Tetratricopeptide repeat; Region: TPR_16; pfam13432 187272004203 TPR motif; other site 187272004204 binding surface 187272004205 Transcriptional regulator [Transcription]; Region: IclR; COG1414 187272004206 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 187272004207 putative DNA binding site [nucleotide binding]; other site 187272004208 putative Zn2+ binding site [ion binding]; other site 187272004209 Bacterial transcriptional regulator; Region: IclR; pfam01614 187272004210 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 187272004211 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 187272004212 MOFRL family; Region: MOFRL; pfam05161 187272004213 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 187272004214 aromatic arch; other site 187272004215 DCoH dimer interaction site [polypeptide binding]; other site 187272004216 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 187272004217 DCoH tetramer interaction site [polypeptide binding]; other site 187272004218 substrate binding site [chemical binding]; other site 187272004219 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 187272004220 trimer interface [polypeptide binding]; other site 187272004221 dimer interface [polypeptide binding]; other site 187272004222 putative active site [active] 187272004223 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 187272004224 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 187272004225 NAD(P) binding site [chemical binding]; other site 187272004226 active site 187272004227 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 187272004228 catalytic core [active] 187272004229 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 187272004230 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; cl17557 187272004231 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 187272004232 putative active site [active] 187272004233 putative metal binding residues [ion binding]; other site 187272004234 signature motif; other site 187272004235 putative dimer interface [polypeptide binding]; other site 187272004236 putative phosphate binding site [ion binding]; other site 187272004237 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 187272004238 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272004239 beta-hexosaminidase; Provisional; Region: PRK05337 187272004240 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 187272004241 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272004242 active site 187272004243 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 187272004244 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 187272004245 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 187272004246 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 187272004247 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 187272004248 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 187272004249 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 187272004250 Iron-sulfur protein interface; other site 187272004251 proximal quinone binding site [chemical binding]; other site 187272004252 SdhD (CybS) interface [polypeptide binding]; other site 187272004253 proximal heme binding site [chemical binding]; other site 187272004254 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 187272004255 putative SdhC subunit interface [polypeptide binding]; other site 187272004256 putative proximal heme binding site [chemical binding]; other site 187272004257 putative Iron-sulfur protein interface [polypeptide binding]; other site 187272004258 putative proximal quinone binding site; other site 187272004259 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 187272004260 L-aspartate oxidase; Provisional; Region: PRK06175 187272004261 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 187272004262 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 187272004263 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 187272004264 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 187272004265 L-aspartate oxidase; Provisional; Region: PRK09077 187272004266 L-aspartate oxidase; Provisional; Region: PRK06175 187272004267 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 187272004268 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 187272004269 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 187272004270 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 187272004271 DNA binding residues [nucleotide binding] 187272004272 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 187272004273 anti-sigma E factor; Provisional; Region: rseB; PRK09455 187272004274 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 187272004275 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 187272004276 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 187272004277 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 187272004278 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 187272004279 protein binding site [polypeptide binding]; other site 187272004280 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 187272004281 protein binding site [polypeptide binding]; other site 187272004282 GTP-binding protein LepA; Provisional; Region: PRK05433 187272004283 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 187272004284 G1 box; other site 187272004285 putative GEF interaction site [polypeptide binding]; other site 187272004286 GTP/Mg2+ binding site [chemical binding]; other site 187272004287 Switch I region; other site 187272004288 G2 box; other site 187272004289 G3 box; other site 187272004290 Switch II region; other site 187272004291 G4 box; other site 187272004292 G5 box; other site 187272004293 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 187272004294 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 187272004295 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 187272004296 signal peptidase I; Provisional; Region: PRK10861 187272004297 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 187272004298 Catalytic site [active] 187272004299 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 187272004300 ribonuclease III; Reviewed; Region: rnc; PRK00102 187272004301 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 187272004302 dimerization interface [polypeptide binding]; other site 187272004303 active site 187272004304 metal binding site [ion binding]; metal-binding site 187272004305 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 187272004306 dsRNA binding site [nucleotide binding]; other site 187272004307 GTPase Era; Reviewed; Region: era; PRK00089 187272004308 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 187272004309 G1 box; other site 187272004310 GTP/Mg2+ binding site [chemical binding]; other site 187272004311 Switch I region; other site 187272004312 G2 box; other site 187272004313 Switch II region; other site 187272004314 G3 box; other site 187272004315 G4 box; other site 187272004316 G5 box; other site 187272004317 KH domain; Region: KH_2; pfam07650 187272004318 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 187272004319 Recombination protein O N terminal; Region: RecO_N; pfam11967 187272004320 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 187272004321 active site 187272004322 hydrophilic channel; other site 187272004323 dimerization interface [polypeptide binding]; other site 187272004324 catalytic residues [active] 187272004325 active site lid [active] 187272004326 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 187272004327 cysteine synthase B; Region: cysM; TIGR01138 187272004328 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 187272004329 dimer interface [polypeptide binding]; other site 187272004330 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272004331 catalytic residue [active] 187272004332 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 187272004333 active site 187272004334 catalytic site [active] 187272004335 substrate binding site [chemical binding]; other site 187272004336 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 187272004337 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 187272004338 TRAM domain; Region: TRAM; cl01282 187272004339 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 187272004340 S-adenosylmethionine binding site [chemical binding]; other site 187272004341 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 187272004342 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 187272004343 dimer interface [polypeptide binding]; other site 187272004344 ADP-ribose binding site [chemical binding]; other site 187272004345 active site 187272004346 nudix motif; other site 187272004347 metal binding site [ion binding]; metal-binding site 187272004348 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 187272004349 adenylosuccinate lyase; Provisional; Region: PRK09285 187272004350 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 187272004351 tetramer interface [polypeptide binding]; other site 187272004352 active site 187272004353 fumarate hydratase; Reviewed; Region: fumC; PRK00485 187272004354 Class II fumarases; Region: Fumarase_classII; cd01362 187272004355 active site 187272004356 tetramer interface [polypeptide binding]; other site 187272004357 RibD C-terminal domain; Region: RibD_C; cl17279 187272004358 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 187272004359 Fe-S cluster binding site [ion binding]; other site 187272004360 DNA binding site [nucleotide binding] 187272004361 active site 187272004362 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 187272004363 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 187272004364 GIY-YIG motif/motif A; other site 187272004365 active site 187272004366 catalytic site [active] 187272004367 putative DNA binding site [nucleotide binding]; other site 187272004368 metal binding site [ion binding]; metal-binding site 187272004369 UvrB/uvrC motif; Region: UVR; pfam02151 187272004370 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 187272004371 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 187272004372 Uncharacterized conserved protein [Function unknown]; Region: COG0398 187272004373 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 187272004374 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 187272004375 short chain dehydrogenase; Provisional; Region: PRK05993 187272004376 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 187272004377 NADP binding site [chemical binding]; other site 187272004378 active site 187272004379 steroid binding site; other site 187272004380 SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell...; Region: S2P-M50_SpoIVFB_CBS; cd06164 187272004381 Peptidase family M50; Region: Peptidase_M50; pfam02163 187272004382 active site 187272004383 putative substrate binding region [chemical binding]; other site 187272004384 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide...; Region: CBS_pair_M50_like; cd04801 187272004385 PAS domain S-box; Region: sensory_box; TIGR00229 187272004386 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 187272004387 putative active site [active] 187272004388 heme pocket [chemical binding]; other site 187272004389 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272004390 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272004391 metal binding site [ion binding]; metal-binding site 187272004392 active site 187272004393 I-site; other site 187272004394 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 187272004395 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272004396 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272004397 Walker A/P-loop; other site 187272004398 ATP binding site [chemical binding]; other site 187272004399 Q-loop/lid; other site 187272004400 ABC transporter signature motif; other site 187272004401 Walker B; other site 187272004402 D-loop; other site 187272004403 H-loop/switch region; other site 187272004404 BCCT family transporter; Region: BCCT; pfam02028 187272004405 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 187272004406 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 187272004407 FeS/SAM binding site; other site 187272004408 HemN C-terminal domain; Region: HemN_C; pfam06969 187272004409 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 187272004410 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 187272004411 dimer interface [polypeptide binding]; other site 187272004412 active site 187272004413 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 187272004414 active site 1 [active] 187272004415 dimer interface [polypeptide binding]; other site 187272004416 active site 2 [active] 187272004417 Domain of unknown function (DUF4168); Region: DUF4168; pfam13767 187272004418 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 187272004419 dimerization interface [polypeptide binding]; other site 187272004420 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 187272004421 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 187272004422 dimer interface [polypeptide binding]; other site 187272004423 phosphorylation site [posttranslational modification] 187272004424 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272004425 ATP binding site [chemical binding]; other site 187272004426 Mg2+ binding site [ion binding]; other site 187272004427 G-X-G motif; other site 187272004428 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272004429 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272004430 active site 187272004431 phosphorylation site [posttranslational modification] 187272004432 intermolecular recognition site; other site 187272004433 dimerization interface [polypeptide binding]; other site 187272004434 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 187272004435 Walker A motif; other site 187272004436 ATP binding site [chemical binding]; other site 187272004437 Walker B motif; other site 187272004438 arginine finger; other site 187272004439 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272004440 lytic murein transglycosylase; Provisional; Region: PRK11619 187272004441 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 187272004442 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272004443 catalytic residue [active] 187272004444 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 187272004445 Predicted membrane protein [Function unknown]; Region: COG2860 187272004446 UPF0126 domain; Region: UPF0126; pfam03458 187272004447 UPF0126 domain; Region: UPF0126; pfam03458 187272004448 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 187272004449 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 187272004450 TPP-binding site; other site 187272004451 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 187272004452 PYR/PP interface [polypeptide binding]; other site 187272004453 dimer interface [polypeptide binding]; other site 187272004454 TPP binding site [chemical binding]; other site 187272004455 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 187272004456 hypothetical protein; Provisional; Region: PRK05170 187272004457 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 187272004458 metal-binding site [ion binding] 187272004459 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 187272004460 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 187272004461 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 187272004462 Predicted membrane protein [Function unknown]; Region: COG3462 187272004463 Short C-terminal domain; Region: SHOCT; pfam09851 187272004464 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 187272004465 dimer interface [polypeptide binding]; other site 187272004466 Outer membrane efflux protein; Region: OEP; pfam02321 187272004467 Outer membrane efflux protein; Region: OEP; pfam02321 187272004468 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 187272004469 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272004470 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 187272004471 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 187272004472 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 187272004473 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 187272004474 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 187272004475 G1 box; other site 187272004476 putative GEF interaction site [polypeptide binding]; other site 187272004477 GTP/Mg2+ binding site [chemical binding]; other site 187272004478 Switch I region; other site 187272004479 G2 box; other site 187272004480 G3 box; other site 187272004481 Switch II region; other site 187272004482 G4 box; other site 187272004483 G5 box; other site 187272004484 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 187272004485 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]; Region: COG1916 187272004486 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 187272004487 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 187272004488 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 187272004489 acyl-activating enzyme (AAE) consensus motif; other site 187272004490 putative AMP binding site [chemical binding]; other site 187272004491 putative active site [active] 187272004492 putative CoA binding site [chemical binding]; other site 187272004493 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 187272004494 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 187272004495 flagellar motor protein MotS; Reviewed; Region: PRK06925 187272004496 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272004497 ligand binding site [chemical binding]; other site 187272004498 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 187272004499 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 187272004500 FMN binding site [chemical binding]; other site 187272004501 active site 187272004502 catalytic residues [active] 187272004503 substrate binding site [chemical binding]; other site 187272004504 glycerate dehydrogenase; Provisional; Region: PRK06487 187272004505 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 187272004506 putative ligand binding site [chemical binding]; other site 187272004507 putative NAD binding site [chemical binding]; other site 187272004508 catalytic site [active] 187272004509 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 187272004510 NAD(P) binding site [chemical binding]; other site 187272004511 active site 187272004512 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 187272004513 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 187272004514 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272004515 LysR family transcriptional regulator; Provisional; Region: PRK14997 187272004516 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 187272004517 putative effector binding pocket; other site 187272004518 dimerization interface [polypeptide binding]; other site 187272004519 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 187272004520 YceI-like domain; Region: YceI; cl01001 187272004521 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 187272004522 S-adenosylmethionine binding site [chemical binding]; other site 187272004523 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 187272004524 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 187272004525 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 187272004526 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 187272004527 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272004528 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 187272004529 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272004530 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 187272004531 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 187272004532 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272004533 ligand binding site [chemical binding]; other site 187272004534 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 187272004535 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 187272004536 putative NAD(P) binding site [chemical binding]; other site 187272004537 putative substrate binding site [chemical binding]; other site 187272004538 catalytic Zn binding site [ion binding]; other site 187272004539 structural Zn binding site [ion binding]; other site 187272004540 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 187272004541 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 187272004542 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 187272004543 catalytic residue [active] 187272004544 PilZ domain; Region: PilZ; cl01260 187272004545 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 187272004546 DNA polymerase III subunit delta'; Validated; Region: PRK08485 187272004547 thymidylate kinase; Validated; Region: tmk; PRK00698 187272004548 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 187272004549 TMP-binding site; other site 187272004550 ATP-binding site [chemical binding]; other site 187272004551 YceG-like family; Region: YceG; pfam02618 187272004552 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 187272004553 dimerization interface [polypeptide binding]; other site 187272004554 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 187272004555 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 187272004556 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272004557 catalytic residue [active] 187272004558 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 187272004559 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 187272004560 dimer interface [polypeptide binding]; other site 187272004561 active site 187272004562 acyl carrier protein; Provisional; Region: acpP; PRK00982 187272004563 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 187272004564 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 187272004565 NAD(P) binding site [chemical binding]; other site 187272004566 homotetramer interface [polypeptide binding]; other site 187272004567 homodimer interface [polypeptide binding]; other site 187272004568 active site 187272004569 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 187272004570 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 187272004571 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 187272004572 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 187272004573 dimer interface [polypeptide binding]; other site 187272004574 active site 187272004575 CoA binding pocket [chemical binding]; other site 187272004576 putative phosphate acyltransferase; Provisional; Region: PRK05331 187272004577 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 187272004578 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 187272004579 Maf-like protein; Region: Maf; pfam02545 187272004580 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 187272004581 active site 187272004582 dimer interface [polypeptide binding]; other site 187272004583 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 187272004584 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 187272004585 tandem repeat interface [polypeptide binding]; other site 187272004586 oligomer interface [polypeptide binding]; other site 187272004587 active site residues [active] 187272004588 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 187272004589 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 187272004590 RNA binding surface [nucleotide binding]; other site 187272004591 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 187272004592 active site 187272004593 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 187272004594 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 187272004595 homodimer interface [polypeptide binding]; other site 187272004596 oligonucleotide binding site [chemical binding]; other site 187272004597 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 187272004598 Low molecular weight phosphatase family; Region: LMWPc; cd00115 187272004599 active site 187272004600 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 187272004601 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 187272004602 Ligand binding site; other site 187272004603 oligomer interface; other site 187272004604 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 187272004605 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 187272004606 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 187272004607 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 187272004608 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 187272004609 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 187272004610 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 187272004611 Competence protein; Region: Competence; pfam03772 187272004612 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 187272004613 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 187272004614 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 187272004615 Walker A/P-loop; other site 187272004616 ATP binding site [chemical binding]; other site 187272004617 Q-loop/lid; other site 187272004618 ABC transporter signature motif; other site 187272004619 Walker B; other site 187272004620 D-loop; other site 187272004621 H-loop/switch region; other site 187272004622 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 187272004623 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 187272004624 FtsX-like permease family; Region: FtsX; pfam02687 187272004625 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 187272004626 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 187272004627 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 187272004628 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 187272004629 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 187272004630 putative active site; other site 187272004631 catalytic triad [active] 187272004632 putative dimer interface [polypeptide binding]; other site 187272004633 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 187272004634 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 187272004635 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 187272004636 rRNA binding site [nucleotide binding]; other site 187272004637 predicted 30S ribosome binding site; other site 187272004638 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 187272004639 Clp amino terminal domain; Region: Clp_N; pfam02861 187272004640 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 187272004641 Walker A motif; other site 187272004642 ATP binding site [chemical binding]; other site 187272004643 Walker B motif; other site 187272004644 arginine finger; other site 187272004645 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 187272004646 Walker A motif; other site 187272004647 ATP binding site [chemical binding]; other site 187272004648 Walker B motif; other site 187272004649 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 187272004650 Uncharacterized conserved protein [Function unknown]; Region: COG2127 187272004651 Transcriptional regulator [Transcription]; Region: LysR; COG0583 187272004652 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272004653 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 187272004654 dimerization interface [polypeptide binding]; other site 187272004655 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 187272004656 nudix motif; other site 187272004657 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 187272004658 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 187272004659 Ligand Binding Site [chemical binding]; other site 187272004660 putative lysogenization regulator; Reviewed; Region: PRK00218 187272004661 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 187272004662 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 187272004663 substrate binding site [chemical binding]; other site 187272004664 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 187272004665 substrate binding site [chemical binding]; other site 187272004666 ligand binding site [chemical binding]; other site 187272004667 aconitate hydratase; Validated; Region: PRK09277 187272004668 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 187272004669 substrate binding site [chemical binding]; other site 187272004670 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 187272004671 ligand binding site [chemical binding]; other site 187272004672 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 187272004673 substrate binding site [chemical binding]; other site 187272004674 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 187272004675 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272004676 ligand binding site [chemical binding]; other site 187272004677 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 187272004678 active site 187272004679 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 187272004680 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 187272004681 homodimer interface [polypeptide binding]; other site 187272004682 metal binding site [ion binding]; metal-binding site 187272004683 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 187272004684 homodimer interface [polypeptide binding]; other site 187272004685 active site 187272004686 putative chemical substrate binding site [chemical binding]; other site 187272004687 metal binding site [ion binding]; metal-binding site 187272004688 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272004689 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272004690 WHG domain; Region: WHG; pfam13305 187272004691 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 187272004692 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 187272004693 C-terminal domain interface [polypeptide binding]; other site 187272004694 GSH binding site (G-site) [chemical binding]; other site 187272004695 dimer interface [polypeptide binding]; other site 187272004696 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 187272004697 N-terminal domain interface [polypeptide binding]; other site 187272004698 dimer interface [polypeptide binding]; other site 187272004699 substrate binding pocket (H-site) [chemical binding]; other site 187272004700 TPR repeat; Region: TPR_11; pfam13414 187272004701 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 187272004702 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 187272004703 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 187272004704 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 187272004705 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 187272004706 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 187272004707 quinone interaction residues [chemical binding]; other site 187272004708 active site 187272004709 catalytic residues [active] 187272004710 FMN binding site [chemical binding]; other site 187272004711 substrate binding site [chemical binding]; other site 187272004712 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 187272004713 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 187272004714 P-loop; other site 187272004715 Magnesium ion binding site [ion binding]; other site 187272004716 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 187272004717 Magnesium ion binding site [ion binding]; other site 187272004718 Transglycosylase SLT domain; Region: SLT_2; pfam13406 187272004719 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 187272004720 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272004721 catalytic residue [active] 187272004722 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 187272004723 Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II; Region: CPT; cl17391 187272004724 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 187272004725 hypothetical protein; Provisional; Region: PRK10279 187272004726 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 187272004727 active site 187272004728 nucleophile elbow; other site 187272004729 TSCPD domain; Region: TSCPD; pfam12637 187272004730 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 187272004731 Ribonucleotide reductase, barrel domain; Region: Ribonuc_red_lgC; pfam02867 187272004732 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 187272004733 protein-splicing catalytic site; other site 187272004734 thioester formation/cholesterol transfer; other site 187272004735 Ribonucleotide reductase, barrel domain; Region: Ribonuc_red_lgC; pfam02867 187272004736 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 187272004737 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 187272004738 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 187272004739 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 187272004740 RNA binding site [nucleotide binding]; other site 187272004741 HrpA-like helicases [DNA replication, recombination, and repair]; Region: HrpA; COG1643 187272004742 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 187272004743 putative Mg++ binding site [ion binding]; other site 187272004744 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 187272004745 nucleotide binding region [chemical binding]; other site 187272004746 ATP-binding site [chemical binding]; other site 187272004747 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 187272004748 Predicted transcriptional regulator [Transcription]; Region: COG2378 187272004749 WYL domain; Region: WYL; pfam13280 187272004750 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 187272004751 carbon storage regulator; Provisional; Region: PRK01712 187272004752 aspartate kinase; Reviewed; Region: PRK06635 187272004753 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 187272004754 putative nucleotide binding site [chemical binding]; other site 187272004755 putative catalytic residues [active] 187272004756 putative Mg ion binding site [ion binding]; other site 187272004757 putative aspartate binding site [chemical binding]; other site 187272004758 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 187272004759 putative allosteric regulatory site; other site 187272004760 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 187272004761 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 187272004762 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 187272004763 motif 1; other site 187272004764 active site 187272004765 motif 2; other site 187272004766 motif 3; other site 187272004767 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 187272004768 DHHA1 domain; Region: DHHA1; pfam02272 187272004769 recombination regulator RecX; Reviewed; Region: recX; PRK00117 187272004770 recombinase A; Provisional; Region: recA; PRK09354 187272004771 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 187272004772 hexamer interface [polypeptide binding]; other site 187272004773 Walker A motif; other site 187272004774 ATP binding site [chemical binding]; other site 187272004775 Walker B motif; other site 187272004776 Competence-damaged protein; Region: CinA; pfam02464 187272004777 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 187272004778 MutS domain I; Region: MutS_I; pfam01624 187272004779 MutS domain II; Region: MutS_II; pfam05188 187272004780 MutS domain III; Region: MutS_III; pfam05192 187272004781 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 187272004782 Walker A/P-loop; other site 187272004783 ATP binding site [chemical binding]; other site 187272004784 Q-loop/lid; other site 187272004785 ABC transporter signature motif; other site 187272004786 Walker B; other site 187272004787 D-loop; other site 187272004788 H-loop/switch region; other site 187272004789 Ferredoxin [Energy production and conversion]; Region: COG1146 187272004790 4Fe-4S binding domain; Region: Fer4; cl02805 187272004791 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 187272004792 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 187272004793 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 187272004794 dimerization domain [polypeptide binding]; other site 187272004795 dimer interface [polypeptide binding]; other site 187272004796 catalytic residues [active] 187272004797 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 187272004798 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 187272004799 active site 187272004800 DNA binding site [nucleotide binding] 187272004801 Int/Topo IB signature motif; other site 187272004802 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 187272004803 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 187272004804 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 187272004805 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 187272004806 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 187272004807 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 187272004808 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272004809 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 187272004810 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 187272004811 heme binding pocket [chemical binding]; other site 187272004812 heme ligand [chemical binding]; other site 187272004813 GAF domain; Region: GAF; pfam01590 187272004814 Phytochrome region; Region: PHY; pfam00360 187272004815 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272004816 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272004817 metal binding site [ion binding]; metal-binding site 187272004818 active site 187272004819 I-site; other site 187272004820 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 187272004821 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272004822 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 187272004823 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 187272004824 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 187272004825 FeS/SAM binding site; other site 187272004826 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 187272004827 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 187272004828 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 187272004829 catalytic site [active] 187272004830 putative active site [active] 187272004831 putative substrate binding site [chemical binding]; other site 187272004832 dimer interface [polypeptide binding]; other site 187272004833 Predicted GTPases [General function prediction only]; Region: COG1162 187272004834 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 187272004835 RNA binding site [nucleotide binding]; other site 187272004836 homodimer interface [polypeptide binding]; other site 187272004837 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 187272004838 GTPase/Zn-binding domain interface [polypeptide binding]; other site 187272004839 GTP/Mg2+ binding site [chemical binding]; other site 187272004840 G4 box; other site 187272004841 G5 box; other site 187272004842 G1 box; other site 187272004843 Switch I region; other site 187272004844 G2 box; other site 187272004845 G3 box; other site 187272004846 Switch II region; other site 187272004847 flagellar motor protein MotB; Validated; Region: motB; PRK09041 187272004848 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272004849 ligand binding site [chemical binding]; other site 187272004850 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 187272004851 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 187272004852 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 187272004853 nucleotide binding site/active site [active] 187272004854 HIT family signature motif; other site 187272004855 catalytic residue [active] 187272004856 recombination protein RecR; Reviewed; Region: recR; PRK00076 187272004857 RecR protein; Region: RecR; pfam02132 187272004858 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 187272004859 putative active site [active] 187272004860 putative metal-binding site [ion binding]; other site 187272004861 tetramer interface [polypeptide binding]; other site 187272004862 hypothetical protein; Validated; Region: PRK00153 187272004863 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 187272004864 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 187272004865 Walker A motif; other site 187272004866 ATP binding site [chemical binding]; other site 187272004867 Walker B motif; other site 187272004868 arginine finger; other site 187272004869 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 187272004870 Haemolytic domain; Region: Haemolytic; pfam01809 187272004871 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272004872 active site residue [active] 187272004873 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 187272004874 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 187272004875 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 187272004876 Putative rRNA methylase; Region: rRNA_methylase; pfam06962 187272004877 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 187272004878 Ligand Binding Site [chemical binding]; other site 187272004879 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 187272004880 AAA domain; Region: AAA_32; pfam13654 187272004881 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 187272004882 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 187272004883 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 187272004884 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 187272004885 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272004886 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272004887 metal binding site [ion binding]; metal-binding site 187272004888 active site 187272004889 I-site; other site 187272004890 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 187272004891 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 187272004892 dimer interface [polypeptide binding]; other site 187272004893 active site 187272004894 heme binding site [chemical binding]; other site 187272004895 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 187272004896 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 187272004897 active site 187272004898 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 187272004899 MPT binding site; other site 187272004900 trimer interface [polypeptide binding]; other site 187272004901 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272004902 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 187272004903 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 187272004904 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 187272004905 Transposase; Region: HTH_Tnp_1; cl17663 187272004906 putative transposase OrfB; Reviewed; Region: PHA02517 187272004907 HTH-like domain; Region: HTH_21; pfam13276 187272004908 Integrase core domain; Region: rve; pfam00665 187272004909 Integrase core domain; Region: rve_2; pfam13333 187272004910 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 187272004911 probable regulatory domain; Region: near_KaiC_dom; TIGR03879 187272004912 Integrase core domain; Region: rve; pfam00665 187272004913 Integrase core domain; Region: rve_3; cl15866 187272004914 transposase; Provisional; Region: PRK06526 187272004915 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 187272004916 Walker A motif; other site 187272004917 ATP binding site [chemical binding]; other site 187272004918 Walker B motif; other site 187272004919 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 187272004920 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 187272004921 Transposase; Region: HTH_Tnp_1; cl17663 187272004922 putative transposase OrfB; Reviewed; Region: PHA02517 187272004923 HTH-like domain; Region: HTH_21; pfam13276 187272004924 Integrase core domain; Region: rve; pfam00665 187272004925 Integrase core domain; Region: rve_2; pfam13333 187272004926 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 187272004927 active site 187272004928 catalytic residues [active] 187272004929 DNA binding site [nucleotide binding] 187272004930 Int/Topo IB signature motif; other site 187272004931 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 187272004932 Transposase; Region: HTH_Tnp_1; cl17663 187272004933 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 187272004934 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 187272004935 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 187272004936 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 187272004937 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 187272004938 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 187272004939 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 187272004940 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4877 187272004941 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 187272004942 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 187272004943 ATP binding site [chemical binding]; other site 187272004944 putative Mg++ binding site [ion binding]; other site 187272004945 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 187272004946 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 187272004947 nucleotide binding region [chemical binding]; other site 187272004948 ATP-binding site [chemical binding]; other site 187272004949 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 187272004950 DNA methylase; Region: N6_N4_Mtase; cl17433 187272004951 DNA methylase; Region: N6_N4_Mtase; cl17433 187272004952 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 187272004953 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 187272004954 active site 187272004955 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272004956 AAA domain; Region: AAA_23; pfam13476 187272004957 Walker A/P-loop; other site 187272004958 ATP binding site [chemical binding]; other site 187272004959 ProQ/FINO family; Region: ProQ; smart00945 187272004960 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272004961 ABC transporter signature motif; other site 187272004962 Walker B; other site 187272004963 D-loop; other site 187272004964 H-loop/switch region; other site 187272004965 Divergent AAA domain; Region: AAA_4; pfam04326 187272004966 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 187272004967 DEAD-like helicases superfamily; Region: DEXDc; smart00487 187272004968 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 187272004969 ATP binding site [chemical binding]; other site 187272004970 putative Mg++ binding site [ion binding]; other site 187272004971 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 187272004972 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 187272004973 metal ion-dependent adhesion site (MIDAS); other site 187272004974 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 187272004975 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 187272004976 Walker A motif; other site 187272004977 ATP binding site [chemical binding]; other site 187272004978 Walker B motif; other site 187272004979 arginine finger; other site 187272004980 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 187272004981 active site 187272004982 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 187272004983 MPT binding site; other site 187272004984 trimer interface [polypeptide binding]; other site 187272004985 SprT homologues; Region: SprT; cl01182 187272004986 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 187272004987 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 187272004988 antiporter inner membrane protein; Provisional; Region: PRK11670 187272004989 Domain of unknown function DUF59; Region: DUF59; pfam01883 187272004990 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 187272004991 Walker A motif; other site 187272004992 SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of Sulfolobus acidocaldarius that combines...; Region: Rieske_SoxF_SoxL; cd03475 187272004993 [2Fe-2S] cluster binding site [ion binding]; other site 187272004994 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 187272004995 MoaE homodimer interface [polypeptide binding]; other site 187272004996 MoaD interaction [polypeptide binding]; other site 187272004997 active site residues [active] 187272004998 cheY-homologous receiver domain; Region: REC; smart00448 187272004999 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272005000 GAF domain; Region: GAF; pfam01590 187272005001 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 187272005002 PAS domain; Region: PAS_9; pfam13426 187272005003 putative active site [active] 187272005004 heme pocket [chemical binding]; other site 187272005005 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 187272005006 PAS domain; Region: PAS_9; pfam13426 187272005007 putative active site [active] 187272005008 heme pocket [chemical binding]; other site 187272005009 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005010 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005011 metal binding site [ion binding]; metal-binding site 187272005012 active site 187272005013 I-site; other site 187272005014 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 187272005015 PAS fold; Region: PAS_4; pfam08448 187272005016 PAS domain; Region: PAS; smart00091 187272005017 putative active site [active] 187272005018 heme pocket [chemical binding]; other site 187272005019 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 187272005020 LytTr DNA-binding domain; Region: LytTR; smart00850 187272005021 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 187272005022 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 187272005023 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 187272005024 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 187272005025 carbon-monoxide dehydrogenase, large subunit; Region: CO_dehy_Mo_lg; TIGR02416 187272005026 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 187272005027 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 187272005028 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_5; cd07823 187272005029 putative hydrophobic ligand binding site [chemical binding]; other site 187272005030 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 187272005031 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 187272005032 Walker A motif; other site 187272005033 ATP binding site [chemical binding]; other site 187272005034 Walker B motif; other site 187272005035 arginine finger; other site 187272005036 VWA domain containing CoxE-like protein; Region: VWA_CoxE; pfam05762 187272005037 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 187272005038 metal ion-dependent adhesion site (MIDAS); other site 187272005039 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 187272005040 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 187272005041 XdhC Rossmann domain; Region: XdhC_C; pfam13478 187272005042 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 187272005043 Ligand binding site; other site 187272005044 metal-binding site 187272005045 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 187272005046 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 187272005047 XdhC Rossmann domain; Region: XdhC_C; pfam13478 187272005048 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 187272005049 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 187272005050 trimerization site [polypeptide binding]; other site 187272005051 active site 187272005052 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 187272005053 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 187272005054 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 187272005055 Walker A motif; other site 187272005056 ATP binding site [chemical binding]; other site 187272005057 Walker B motif; other site 187272005058 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 187272005059 PAS fold; Region: PAS_3; pfam08447 187272005060 putative active site [active] 187272005061 heme pocket [chemical binding]; other site 187272005062 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 187272005063 PAS domain; Region: PAS_9; pfam13426 187272005064 putative active site [active] 187272005065 heme pocket [chemical binding]; other site 187272005066 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005067 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005068 active site 187272005069 I-site; other site 187272005070 metal binding site [ion binding]; metal-binding site 187272005071 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272005072 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272005073 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 187272005074 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 187272005075 FtsX-like permease family; Region: FtsX; pfam02687 187272005076 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 187272005077 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 187272005078 Walker A/P-loop; other site 187272005079 ATP binding site [chemical binding]; other site 187272005080 Q-loop/lid; other site 187272005081 ABC transporter signature motif; other site 187272005082 Walker B; other site 187272005083 D-loop; other site 187272005084 H-loop/switch region; other site 187272005085 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 187272005086 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 187272005087 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 187272005088 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272005089 acyl-activating enzyme (AAE) consensus motif; other site 187272005090 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272005091 AMP binding site [chemical binding]; other site 187272005092 active site 187272005093 acyl-activating enzyme (AAE) consensus motif; other site 187272005094 CoA binding site [chemical binding]; other site 187272005095 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 187272005096 active site 187272005097 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 187272005098 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 187272005099 FMN binding site [chemical binding]; other site 187272005100 active site 187272005101 catalytic residues [active] 187272005102 substrate binding site [chemical binding]; other site 187272005103 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 187272005104 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272005105 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272005106 L,D-transpeptidase; Provisional; Region: PRK10260 187272005107 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 187272005108 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 187272005109 putative active site [active] 187272005110 putative CoA binding site [chemical binding]; other site 187272005111 nudix motif; other site 187272005112 metal binding site [ion binding]; metal-binding site 187272005113 lipoyl synthase; Provisional; Region: PRK05481 187272005114 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 187272005115 FeS/SAM binding site; other site 187272005116 Protein of unknown function, DUF399; Region: DUF399; pfam04187 187272005117 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 187272005118 protein binding site [polypeptide binding]; other site 187272005119 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 187272005120 High potential iron-sulfur protein; Region: HIPIP; pfam01355 187272005121 High potential iron-sulfur protein; Region: HIPIP; pfam01355 187272005122 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 187272005123 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272005124 aminopeptidase N; Provisional; Region: pepN; PRK14015 187272005125 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 187272005126 active site 187272005127 Zn binding site [ion binding]; other site 187272005128 carboxy-terminal protease; Provisional; Region: PRK11186 187272005129 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 187272005130 protein binding site [polypeptide binding]; other site 187272005131 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 187272005132 Catalytic dyad [active] 187272005133 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 187272005134 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 187272005135 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 187272005136 substrate binding site [chemical binding]; other site 187272005137 oxyanion hole (OAH) forming residues; other site 187272005138 trimer interface [polypeptide binding]; other site 187272005139 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 187272005140 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 187272005141 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 187272005142 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 187272005143 G1 box; other site 187272005144 GTP/Mg2+ binding site [chemical binding]; other site 187272005145 G2 box; other site 187272005146 Switch I region; other site 187272005147 G3 box; other site 187272005148 Switch II region; other site 187272005149 G4 box; other site 187272005150 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 187272005151 G1 box; other site 187272005152 GTP/Mg2+ binding site [chemical binding]; other site 187272005153 G2 box; other site 187272005154 Switch I region; other site 187272005155 G3 box; other site 187272005156 Switch II region; other site 187272005157 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 187272005158 AMP-binding enzyme; Region: AMP-binding; pfam00501 187272005159 acyl-activating enzyme (AAE) consensus motif; other site 187272005160 putative AMP binding site [chemical binding]; other site 187272005161 putative active site [active] 187272005162 putative CoA binding site [chemical binding]; other site 187272005163 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 187272005164 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 187272005165 putative acyl-acceptor binding pocket; other site 187272005166 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 187272005167 PAP2 superfamily; Region: PAP2; pfam01569 187272005168 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 187272005169 Walker A motif; other site 187272005170 Domain of unknown function (DUF3524); Region: DUF3524; pfam12038 187272005171 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 187272005172 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 187272005173 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 187272005174 catalytic triad [active] 187272005175 Smr domain; Region: Smr; pfam01713 187272005176 hypothetical protein; Provisional; Region: PRK09256 187272005177 Predicted integral membrane protein [Function unknown]; Region: COG5615 187272005178 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 187272005179 S-adenosylmethionine binding site [chemical binding]; other site 187272005180 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 187272005181 helicase 45; Provisional; Region: PTZ00424 187272005182 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 187272005183 ATP binding site [chemical binding]; other site 187272005184 Mg++ binding site [ion binding]; other site 187272005185 motif III; other site 187272005186 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 187272005187 nucleotide binding region [chemical binding]; other site 187272005188 ATP-binding site [chemical binding]; other site 187272005189 Site-specific recombinase; Region: SpecificRecomb; pfam10136 187272005190 cystathionine gamma-synthase; Provisional; Region: PRK08249 187272005191 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 187272005192 homodimer interface [polypeptide binding]; other site 187272005193 substrate-cofactor binding pocket; other site 187272005194 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005195 catalytic residue [active] 187272005196 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 187272005197 substrate binding site [chemical binding]; other site 187272005198 KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part...; Region: KaiB_like; cd02978 187272005199 tetramer interface [polypeptide binding]; other site 187272005200 dimer interface [polypeptide binding]; other site 187272005201 PAS domain S-box; Region: sensory_box; TIGR00229 187272005202 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 187272005203 putative active site [active] 187272005204 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005205 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005206 metal binding site [ion binding]; metal-binding site 187272005207 active site 187272005208 I-site; other site 187272005209 PAS domain S-box; Region: sensory_box; TIGR00229 187272005210 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 187272005211 putative active site [active] 187272005212 heme pocket [chemical binding]; other site 187272005213 PAS domain S-box; Region: sensory_box; TIGR00229 187272005214 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 187272005215 putative active site [active] 187272005216 heme pocket [chemical binding]; other site 187272005217 GAF domain; Region: GAF_3; pfam13492 187272005218 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005219 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005220 metal binding site [ion binding]; metal-binding site 187272005221 active site 187272005222 I-site; other site 187272005223 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 187272005224 dimer interface [polypeptide binding]; other site 187272005225 phosphorylation site [posttranslational modification] 187272005226 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005227 ATP binding site [chemical binding]; other site 187272005228 Mg2+ binding site [ion binding]; other site 187272005229 G-X-G motif; other site 187272005230 Response regulator receiver domain; Region: Response_reg; pfam00072 187272005231 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005232 active site 187272005233 phosphorylation site [posttranslational modification] 187272005234 intermolecular recognition site; other site 187272005235 dimerization interface [polypeptide binding]; other site 187272005236 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 187272005237 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 187272005238 DNA binding residues [nucleotide binding] 187272005239 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005241 metal binding site [ion binding]; metal-binding site 187272005242 active site 187272005243 I-site; other site 187272005244 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 187272005245 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 187272005246 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 187272005247 Uncharacterized conserved protein [Function unknown]; Region: COG2128 187272005248 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 187272005249 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 187272005250 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 187272005251 ATP binding site [chemical binding]; other site 187272005252 putative Mg++ binding site [ion binding]; other site 187272005253 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 187272005254 nucleotide binding region [chemical binding]; other site 187272005255 ATP-binding site [chemical binding]; other site 187272005256 Helicase associated domain (HA2); Region: HA2; pfam04408 187272005257 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 187272005258 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 187272005259 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 187272005260 active site 187272005261 metal binding site [ion binding]; metal-binding site 187272005262 homotetramer interface [polypeptide binding]; other site 187272005263 phosphoserine phosphatase; Provisional; Region: thrH; PRK13582 187272005264 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 187272005265 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 187272005266 YccA-like proteins; Region: YccA_like; cd10433 187272005267 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 187272005268 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 187272005269 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 187272005270 Methyltransferase domain; Region: Methyltransf_31; pfam13847 187272005271 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 187272005272 S-adenosylmethionine binding site [chemical binding]; other site 187272005273 RNA polymerase sigma-70 factor, TIGR02947 family; Region: SigH_actino 187272005274 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 187272005275 DNA binding residues [nucleotide binding] 187272005276 mycothiol system anti-sigma-R factor; Region: antisig_RsrA; cl15806 187272005277 Methyltransferase domain; Region: Methyltransf_31; pfam13847 187272005278 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 187272005279 S-adenosylmethionine binding site [chemical binding]; other site 187272005280 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 187272005281 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 187272005282 catalytic triad [active] 187272005283 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 187272005284 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 187272005285 FAD binding domain; Region: FAD_binding_4; pfam01565 187272005286 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 187272005287 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 187272005288 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 187272005289 Cysteine-rich domain; Region: CCG; pfam02754 187272005290 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 187272005291 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 187272005292 putative efflux protein, MATE family; Region: matE; TIGR00797 187272005293 Bifunctional nuclease; Region: DNase-RNase; pfam02577 187272005294 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 187272005295 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 187272005296 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005297 active site 187272005298 phosphorylation site [posttranslational modification] 187272005299 intermolecular recognition site; other site 187272005300 dimerization interface [polypeptide binding]; other site 187272005301 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272005302 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 187272005303 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 187272005304 dimer interface [polypeptide binding]; other site 187272005305 phosphorylation site [posttranslational modification] 187272005306 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005307 ATP binding site [chemical binding]; other site 187272005308 G-X-G motif; other site 187272005309 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 187272005310 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272005311 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272005312 Walker A/P-loop; other site 187272005313 ATP binding site [chemical binding]; other site 187272005314 Q-loop/lid; other site 187272005315 ABC transporter signature motif; other site 187272005316 Walker B; other site 187272005317 D-loop; other site 187272005318 H-loop/switch region; other site 187272005319 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 187272005320 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272005321 Walker A/P-loop; other site 187272005322 ATP binding site [chemical binding]; other site 187272005323 Q-loop/lid; other site 187272005324 ABC transporter signature motif; other site 187272005325 Walker B; other site 187272005326 D-loop; other site 187272005327 H-loop/switch region; other site 187272005328 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 187272005329 PAS domain; Region: PAS_9; pfam13426 187272005330 putative active site [active] 187272005331 heme pocket [chemical binding]; other site 187272005332 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 187272005333 PAS domain; Region: PAS_9; pfam13426 187272005334 putative active site [active] 187272005335 heme pocket [chemical binding]; other site 187272005336 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005337 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005338 metal binding site [ion binding]; metal-binding site 187272005339 active site 187272005340 I-site; other site 187272005341 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 187272005342 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 187272005343 active site 187272005344 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 187272005345 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 187272005346 active site residue [active] 187272005347 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 187272005348 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 187272005349 active site residue [active] 187272005350 Protein of unknown function (DUF3050); Region: DUF3050; pfam11251 187272005351 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09733 187272005352 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 187272005353 active site 187272005354 iron coordination sites [ion binding]; other site 187272005355 substrate binding pocket [chemical binding]; other site 187272005356 sulfite reductase, dissimilatory-type alpha subunit; Region: dsrA; TIGR02064 187272005357 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 187272005358 sulfite reductase, dissimilatory-type beta subunit; Region: dsrB; TIGR02066 187272005359 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 187272005360 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 187272005361 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 187272005362 DsrH like protein; Region: DsrH; pfam04077 187272005363 DsrC like protein; Region: DsrC; pfam04358 187272005364 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 187272005365 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 187272005366 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 187272005367 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 187272005368 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 187272005369 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272005370 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 187272005371 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 187272005372 4Fe-4S binding domain; Region: Fer4; cl02805 187272005373 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 187272005374 hypothetical protein; Validated; Region: PRK09071 187272005375 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 187272005376 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 187272005377 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 187272005378 catalytic triad [active] 187272005379 Predicted transporter component [General function prediction only]; Region: COG2391 187272005380 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 187272005381 Sulphur transport; Region: Sulf_transp; pfam04143 187272005382 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 187272005383 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 187272005384 Sulfate transporter family; Region: Sulfate_transp; pfam00916 187272005385 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 187272005386 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 187272005387 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005388 active site 187272005389 phosphorylation site [posttranslational modification] 187272005390 intermolecular recognition site; other site 187272005391 dimerization interface [polypeptide binding]; other site 187272005392 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 187272005393 DNA binding residues [nucleotide binding] 187272005394 dimerization interface [polypeptide binding]; other site 187272005395 TIGR03089 family protein; Region: TIGR03089 187272005396 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272005397 GAF domain; Region: GAF_3; pfam13492 187272005398 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005399 ATP binding site [chemical binding]; other site 187272005400 Mg2+ binding site [ion binding]; other site 187272005401 G-X-G motif; other site 187272005402 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 187272005403 CPxP motif; other site 187272005404 Cytochrome c; Region: Cytochrom_C; cl11414 187272005405 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 187272005406 Cytochrome c; Region: Cytochrom_C; pfam00034 187272005407 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 187272005408 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 187272005409 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 187272005410 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 187272005411 molybdopterin cofactor binding site; other site 187272005412 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 187272005413 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is...; Region: MopB_CT_2; cd02783 187272005414 putative molybdopterin cofactor binding site; other site 187272005415 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 187272005416 4Fe-4S binding domain; Region: Fer4; pfam00037 187272005417 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 187272005418 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 187272005419 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 187272005420 siroheme synthase; Provisional; Region: cysG; PRK10637 187272005421 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 187272005422 Putative NAD(P)-binding; Region: NAD_binding_7; cl17660 187272005423 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 187272005424 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 187272005425 active site 187272005426 SAM binding site [chemical binding]; other site 187272005427 homodimer interface [polypeptide binding]; other site 187272005428 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272005429 active site residue [active] 187272005430 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 187272005431 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 187272005432 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272005433 Walker A/P-loop; other site 187272005434 ATP binding site [chemical binding]; other site 187272005435 ABC transporter; Region: ABC_tran; pfam00005 187272005436 Q-loop/lid; other site 187272005437 ABC transporter signature motif; other site 187272005438 Walker B; other site 187272005439 D-loop; other site 187272005440 H-loop/switch region; other site 187272005441 CcmB protein; Region: CcmB; cl17444 187272005442 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 187272005443 CcmE; Region: CcmE; pfam03100 187272005444 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 187272005445 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 187272005446 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272005447 catalytic residues [active] 187272005448 central insert; other site 187272005449 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 187272005450 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 187272005451 TPR repeat; Region: TPR_11; pfam13414 187272005452 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 187272005453 binding surface 187272005454 TPR motif; other site 187272005455 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 187272005456 putative active site [active] 187272005457 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 187272005458 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 187272005459 Family description; Region: UvrD_C_2; pfam13538 187272005460 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 187272005461 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 187272005462 HAMP domain; Region: HAMP; pfam00672 187272005463 dimerization interface [polypeptide binding]; other site 187272005464 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 187272005465 dimer interface [polypeptide binding]; other site 187272005466 phosphorylation site [posttranslational modification] 187272005467 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005468 ATP binding site [chemical binding]; other site 187272005469 G-X-G motif; other site 187272005470 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272005471 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005472 active site 187272005473 phosphorylation site [posttranslational modification] 187272005474 intermolecular recognition site; other site 187272005475 dimerization interface [polypeptide binding]; other site 187272005476 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 187272005477 Walker A motif; other site 187272005478 ATP binding site [chemical binding]; other site 187272005479 Walker B motif; other site 187272005480 arginine finger; other site 187272005481 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272005482 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 187272005483 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272005484 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 187272005485 substrate binding site [chemical binding]; other site 187272005486 dimerization interface [polypeptide binding]; other site 187272005487 seryl-tRNA synthetase; Provisional; Region: PRK05431 187272005488 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 187272005489 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 187272005490 dimer interface [polypeptide binding]; other site 187272005491 active site 187272005492 motif 1; other site 187272005493 motif 2; other site 187272005494 motif 3; other site 187272005495 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 187272005496 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272005497 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272005498 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 187272005499 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 187272005500 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 187272005501 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 187272005502 [2Fe-2S] cluster binding site [ion binding]; other site 187272005503 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 187272005504 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 187272005505 [4Fe-4S] binding site [ion binding]; other site 187272005506 molybdopterin cofactor binding site; other site 187272005507 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 187272005508 molybdopterin cofactor binding site; other site 187272005509 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 187272005510 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 187272005511 NMT1-like family; Region: NMT1_2; pfam13379 187272005512 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 187272005513 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 187272005514 dimer interface [polypeptide binding]; other site 187272005515 conserved gate region; other site 187272005516 putative PBP binding loops; other site 187272005517 ABC-ATPase subunit interface; other site 187272005518 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 187272005519 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 187272005520 Walker A/P-loop; other site 187272005521 ATP binding site [chemical binding]; other site 187272005522 Q-loop/lid; other site 187272005523 ABC transporter signature motif; other site 187272005524 Walker B; other site 187272005525 D-loop; other site 187272005526 H-loop/switch region; other site 187272005527 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 187272005528 Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis]; Region: DPH5; COG1798 187272005529 active site 187272005530 SAM binding site [chemical binding]; other site 187272005531 homodimer interface [polypeptide binding]; other site 187272005532 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 187272005533 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 187272005534 active site 187272005535 Nitrate and nitrite sensing; Region: NIT; pfam08376 187272005536 ANTAR domain; Region: ANTAR; pfam03861 187272005537 Predicted membrane protein [Function unknown]; Region: COG3650 187272005538 recombination factor protein RarA; Reviewed; Region: PRK13342 187272005539 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 187272005540 Walker A motif; other site 187272005541 ATP binding site [chemical binding]; other site 187272005542 Walker B motif; other site 187272005543 arginine finger; other site 187272005544 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 187272005545 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 187272005546 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 187272005547 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 187272005548 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 187272005549 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 187272005550 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 187272005551 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 187272005552 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 187272005553 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 187272005554 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 187272005555 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 187272005556 CoenzymeA binding site [chemical binding]; other site 187272005557 subunit interaction site [polypeptide binding]; other site 187272005558 PHB binding site; other site 187272005559 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 187272005560 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 187272005561 dimer interface [polypeptide binding]; other site 187272005562 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005563 catalytic residue [active] 187272005564 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 187272005565 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 187272005566 active site 187272005567 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 187272005568 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 187272005569 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 187272005570 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like2; cd03895 187272005571 acetylornithine deacetylase; Validated; Region: PRK06915 187272005572 metal binding site [ion binding]; metal-binding site 187272005573 dimer interface [polypeptide binding]; other site 187272005574 Predicted acyl esterases [General function prediction only]; Region: COG2936 187272005575 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; smart00939 187272005576 ATP-grasp domain; Region: ATP-grasp_4; cl17255 187272005577 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 187272005578 HI0933-like protein; Region: HI0933_like; pfam03486 187272005579 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 187272005580 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 187272005581 putative active site [active] 187272005582 putative dimer interface [polypeptide binding]; other site 187272005583 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_8; cd06905 187272005584 putative active site [active] 187272005585 Zn binding site [ion binding]; other site 187272005586 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 187272005587 hypothetical protein; Reviewed; Region: PRK09588 187272005588 Archease protein family (MTH1598/TM1083); Region: Archease; pfam01951 187272005589 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 187272005590 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 187272005591 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272005592 active site 187272005593 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 187272005594 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272005595 active site 187272005596 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 187272005597 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 187272005598 putative active site [active] 187272005599 putative metal binding site [ion binding]; other site 187272005600 endonuclease IV; Provisional; Region: PRK01060 187272005601 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 187272005602 AP (apurinic/apyrimidinic) site pocket; other site 187272005603 DNA interaction; other site 187272005604 Metal-binding active site; metal-binding site 187272005605 hypothetical protein; Provisional; Region: PRK07907 187272005606 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 187272005607 metal binding site [ion binding]; metal-binding site 187272005608 putative dimer interface [polypeptide binding]; other site 187272005609 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 187272005610 PhoU domain; Region: PhoU; pfam01895 187272005611 PhoU domain; Region: PhoU; pfam01895 187272005612 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 187272005613 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 187272005614 FOG: CBS domain [General function prediction only]; Region: COG0517 187272005615 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 187272005616 Domain of unknown function (DUF4157); Region: DUF4157; pfam13699 187272005617 DNA/RNA non-specific endonuclease; Region: Endonuclea_NS_2; cl17626 187272005618 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 187272005619 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 187272005620 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 187272005621 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 187272005622 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 187272005623 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 187272005624 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 187272005625 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 187272005626 Walker A motif; other site 187272005627 ATP binding site [chemical binding]; other site 187272005628 Walker B motif; other site 187272005629 arginine finger; other site 187272005630 Protein of unknown function (DUF4255); Region: DUF4255; pfam14065 187272005631 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 187272005632 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 187272005633 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 187272005634 UbiA prenyltransferase family; Region: UbiA; pfam01040 187272005635 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 187272005636 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 187272005637 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 187272005638 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 187272005639 active site 187272005640 nucleophile elbow; other site 187272005641 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 187272005642 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_M15_4; pfam13539 187272005643 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 187272005644 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 187272005645 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 187272005646 Protein of unknown function, DUF547; Region: DUF547; pfam04784 187272005647 Citrate transporter; Region: CitMHS; pfam03600 187272005648 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 187272005649 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 187272005650 nucleophile elbow; other site 187272005651 Protein of unknown function (DUF3185); Region: DUF3185; pfam11381 187272005652 valine--pyruvate transaminase; Provisional; Region: avtA; PRK09440 187272005653 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 187272005654 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005655 homodimer interface [polypeptide binding]; other site 187272005656 catalytic residue [active] 187272005657 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 187272005658 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 187272005659 Cl- selectivity filter; other site 187272005660 Cl- binding residues [ion binding]; other site 187272005661 pore gating glutamate residue; other site 187272005662 dimer interface [polypeptide binding]; other site 187272005663 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272005664 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 187272005665 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 187272005666 The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of...; Region: Delta12-FADS-like; cd03507 187272005667 putative di-iron ligands [ion binding]; other site 187272005668 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 187272005669 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 187272005670 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 187272005671 Coenzyme A binding pocket [chemical binding]; other site 187272005672 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 187272005673 dimerization interface [polypeptide binding]; other site 187272005674 putative DNA binding site [nucleotide binding]; other site 187272005675 putative Zn2+ binding site [ion binding]; other site 187272005676 Uncharacterized conserved protein [Function unknown]; Region: COG3791 187272005677 Domain of unknown function DUF302; Region: DUF302; pfam03625 187272005678 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 187272005679 SelR domain; Region: SelR; pfam01641 187272005680 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 187272005681 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 187272005682 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 187272005683 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 187272005684 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 187272005685 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 187272005686 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 187272005687 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 187272005688 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 187272005689 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 187272005690 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 187272005691 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 187272005692 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 187272005693 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 187272005694 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 187272005695 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 187272005696 ATP binding site [chemical binding]; other site 187272005697 putative Mg++ binding site [ion binding]; other site 187272005698 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 187272005699 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 187272005700 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 187272005701 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 187272005702 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 187272005703 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 187272005704 HsdM N-terminal domain; Region: HsdM_N; pfam12161 187272005705 Methyltransferase domain; Region: Methyltransf_26; pfam13659 187272005706 Protein of unknown function (DUF867); Region: DUF867; pfam05908 187272005707 Protein of unknown function DUF262; Region: DUF262; pfam03235 187272005708 Uncharacterized conserved protein [Function unknown]; Region: COG1479 187272005709 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 187272005710 Putative transposase; Region: Y2_Tnp; pfam04986 187272005711 integron integrase; Region: integrase_gron; TIGR02249 187272005712 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 187272005713 Int/Topo IB signature motif; other site 187272005714 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 187272005715 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 187272005716 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 187272005717 ATP binding site [chemical binding]; other site 187272005718 putative Mg++ binding site [ion binding]; other site 187272005719 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 187272005720 nucleotide binding region [chemical binding]; other site 187272005721 ATP-binding site [chemical binding]; other site 187272005722 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 187272005723 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 187272005724 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272005725 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 187272005726 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 187272005727 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 187272005728 dimer interface [polypeptide binding]; other site 187272005729 phosphorylation site [posttranslational modification] 187272005730 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005731 ATP binding site [chemical binding]; other site 187272005732 Mg2+ binding site [ion binding]; other site 187272005733 G-X-G motif; other site 187272005734 Response regulator receiver domain; Region: Response_reg; pfam00072 187272005735 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005736 active site 187272005737 phosphorylation site [posttranslational modification] 187272005738 intermolecular recognition site; other site 187272005739 dimerization interface [polypeptide binding]; other site 187272005740 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 187272005741 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 187272005742 dimer interface [polypeptide binding]; other site 187272005743 putative anticodon binding site; other site 187272005744 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 187272005745 motif 1; other site 187272005746 active site 187272005747 motif 2; other site 187272005748 motif 3; other site 187272005749 peptide chain release factor 2; Validated; Region: prfB; PRK00578 187272005750 This domain is found in peptide chain release factors; Region: PCRF; smart00937 187272005751 RF-1 domain; Region: RF-1; pfam00472 187272005752 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005753 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005754 metal binding site [ion binding]; metal-binding site 187272005755 active site 187272005756 I-site; other site 187272005757 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 187272005758 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 187272005759 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 187272005760 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 187272005761 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 187272005762 active site 187272005763 HIGH motif; other site 187272005764 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 187272005765 KMSKS motif; other site 187272005766 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 187272005767 tRNA binding surface [nucleotide binding]; other site 187272005768 anticodon binding site; other site 187272005769 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272005770 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 187272005771 active site 187272005772 HIGH motif; other site 187272005773 nucleotide binding site [chemical binding]; other site 187272005774 active site 187272005775 KMSKS motif; other site 187272005776 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 187272005777 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 187272005778 putative active site [active] 187272005779 putative metal binding site [ion binding]; other site 187272005780 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 187272005781 substrate binding site [chemical binding]; other site 187272005782 ATP binding site [chemical binding]; other site 187272005783 Protein of unknown function (DUF461); Region: DUF461; pfam04314 187272005784 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 187272005785 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272005786 Cu(I) binding site [ion binding]; other site 187272005787 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 187272005788 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 187272005789 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 187272005790 DHH family; Region: DHH; pfam01368 187272005791 DHHA1 domain; Region: DHHA1; pfam02272 187272005792 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 187272005793 threonine synthase; Reviewed; Region: PRK06721 187272005794 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 187272005795 homodimer interface [polypeptide binding]; other site 187272005796 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005797 catalytic residue [active] 187272005798 homoserine dehydrogenase; Provisional; Region: PRK06349 187272005799 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 187272005800 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 187272005801 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 187272005802 aminotransferase; Validated; Region: PRK08175 187272005803 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 187272005804 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005805 homodimer interface [polypeptide binding]; other site 187272005806 catalytic residue [active] 187272005807 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 187272005808 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 187272005809 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 187272005810 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 187272005811 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 187272005812 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 187272005813 DNA binding residues [nucleotide binding] 187272005814 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 187272005815 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272005816 Peptidase family M23; Region: Peptidase_M23; pfam01551 187272005817 Predicted membrane protein [Function unknown]; Region: COG1238 187272005818 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 187272005819 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 187272005820 S-adenosylmethionine binding site [chemical binding]; other site 187272005821 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 187272005822 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 187272005823 Smr domain; Region: Smr; pfam01713 187272005824 PAS fold; Region: PAS; pfam00989 187272005825 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 187272005826 putative active site [active] 187272005827 heme pocket [chemical binding]; other site 187272005828 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272005829 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272005830 metal binding site [ion binding]; metal-binding site 187272005831 active site 187272005832 I-site; other site 187272005833 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 187272005834 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272005835 active site 187272005836 phosphorylation site [posttranslational modification] 187272005837 intermolecular recognition site; other site 187272005838 dimerization interface [polypeptide binding]; other site 187272005839 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 187272005840 dimerization interface [polypeptide binding]; other site 187272005841 DNA binding residues [nucleotide binding] 187272005842 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 187272005843 PAS domain; Region: PAS_9; pfam13426 187272005844 putative active site [active] 187272005845 heme pocket [chemical binding]; other site 187272005846 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 187272005847 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 187272005848 dimer interface [polypeptide binding]; other site 187272005849 phosphorylation site [posttranslational modification] 187272005850 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272005851 ATP binding site [chemical binding]; other site 187272005852 Mg2+ binding site [ion binding]; other site 187272005853 G-X-G motif; other site 187272005854 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 187272005855 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 187272005856 DNA binding residues [nucleotide binding] 187272005857 dimerization interface [polypeptide binding]; other site 187272005858 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 187272005859 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 187272005860 Permutation of conserved domain; other site 187272005861 active site 187272005862 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 187272005863 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 187272005864 homotrimer interaction site [polypeptide binding]; other site 187272005865 zinc binding site [ion binding]; other site 187272005866 CDP-binding sites; other site 187272005867 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 187272005868 substrate binding site; other site 187272005869 dimer interface; other site 187272005870 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 187272005871 Septum formation initiator; Region: DivIC; cl17659 187272005872 enolase; Provisional; Region: eno; PRK00077 187272005873 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 187272005874 dimer interface [polypeptide binding]; other site 187272005875 metal binding site [ion binding]; metal-binding site 187272005876 substrate binding pocket [chemical binding]; other site 187272005877 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 187272005878 CTP synthetase; Validated; Region: pyrG; PRK05380 187272005879 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 187272005880 Catalytic site [active] 187272005881 active site 187272005882 UTP binding site [chemical binding]; other site 187272005883 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 187272005884 active site 187272005885 putative oxyanion hole; other site 187272005886 catalytic triad [active] 187272005887 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 187272005888 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 187272005889 Ligand Binding Site [chemical binding]; other site 187272005890 TilS substrate binding domain; Region: TilS; pfam09179 187272005891 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 187272005892 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 187272005893 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 187272005894 PilZ domain; Region: PilZ; pfam07238 187272005895 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 187272005896 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 187272005897 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 187272005898 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 187272005899 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 187272005900 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 187272005901 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 187272005902 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 187272005903 putative active site [active] 187272005904 putative PHP Thumb interface [polypeptide binding]; other site 187272005905 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 187272005906 generic binding surface I; other site 187272005907 generic binding surface II; other site 187272005908 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 187272005909 RNA/DNA hybrid binding site [nucleotide binding]; other site 187272005910 active site 187272005911 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 187272005912 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 187272005913 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 187272005914 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 187272005915 active site 187272005916 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 187272005917 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 187272005918 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 187272005919 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272005920 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272005921 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272005922 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272005923 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 187272005924 Surface antigen; Region: Bac_surface_Ag; pfam01103 187272005925 zinc metallopeptidase RseP; Provisional; Region: PRK10779 187272005926 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 187272005927 active site 187272005928 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 187272005929 protein binding site [polypeptide binding]; other site 187272005930 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 187272005931 protein binding site [polypeptide binding]; other site 187272005932 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 187272005933 putative substrate binding region [chemical binding]; other site 187272005934 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 187272005935 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 187272005936 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 187272005937 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 187272005938 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 187272005939 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 187272005940 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; cd00475 187272005941 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 187272005942 catalytic residue [active] 187272005943 putative FPP diphosphate binding site; other site 187272005944 putative FPP binding hydrophobic cleft; other site 187272005945 dimer interface [polypeptide binding]; other site 187272005946 putative IPP diphosphate binding site; other site 187272005947 ribosome recycling factor; Reviewed; Region: frr; PRK00083 187272005948 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 187272005949 hinge region; other site 187272005950 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 187272005951 putative nucleotide binding site [chemical binding]; other site 187272005952 uridine monophosphate binding site [chemical binding]; other site 187272005953 homohexameric interface [polypeptide binding]; other site 187272005954 elongation factor Ts; Provisional; Region: tsf; PRK09377 187272005955 UBA/TS-N domain; Region: UBA; pfam00627 187272005956 Elongation factor TS; Region: EF_TS; pfam00889 187272005957 Elongation factor TS; Region: EF_TS; pfam00889 187272005958 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 187272005959 rRNA interaction site [nucleotide binding]; other site 187272005960 S8 interaction site; other site 187272005961 putative laminin-1 binding site; other site 187272005962 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 187272005963 active site 187272005964 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 187272005965 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272005966 metal binding triad; other site 187272005967 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 187272005968 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 187272005969 Zn2+ binding site [ion binding]; other site 187272005970 Mg2+ binding site [ion binding]; other site 187272005971 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 187272005972 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 187272005973 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 187272005974 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 187272005975 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272005976 homodimer interface [polypeptide binding]; other site 187272005977 catalytic residue [active] 187272005978 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 187272005979 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 187272005980 trimer interface [polypeptide binding]; other site 187272005981 active site 187272005982 substrate binding site [chemical binding]; other site 187272005983 CoA binding site [chemical binding]; other site 187272005984 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 187272005985 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 187272005986 metal binding site [ion binding]; metal-binding site 187272005987 dimer interface [polypeptide binding]; other site 187272005988 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 187272005989 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 187272005990 polyphosphate kinase; Provisional; Region: PRK05443 187272005991 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 187272005992 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 187272005993 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 187272005994 putative active site [active] 187272005995 catalytic site [active] 187272005996 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 187272005997 putative domain interface [polypeptide binding]; other site 187272005998 putative active site [active] 187272005999 catalytic site [active] 187272006000 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 187272006001 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 187272006002 nucleotide binding site [chemical binding]; other site 187272006003 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 187272006004 catalytic core [active] 187272006005 HDOD domain; Region: HDOD; pfam08668 187272006006 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272006007 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272006008 metal binding site [ion binding]; metal-binding site 187272006009 active site 187272006010 I-site; other site 187272006011 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 187272006012 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 187272006013 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 187272006014 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 187272006015 metal-binding site [ion binding] 187272006016 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 187272006017 Soluble P-type ATPase [General function prediction only]; Region: COG4087 187272006018 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 187272006019 FixH; Region: FixH; pfam05751 187272006020 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 187272006021 4Fe-4S binding domain; Region: Fer4_5; pfam12801 187272006022 4Fe-4S binding domain; Region: Fer4; pfam00037 187272006023 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 187272006024 Peroxin 13, N-terminal region; Region: Peroxin-13_N; pfam04088 187272006025 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 187272006026 Cytochrome c; Region: Cytochrom_C; pfam00034 187272006027 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 187272006028 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 187272006029 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 187272006030 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 187272006031 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 187272006032 Low-spin heme binding site [chemical binding]; other site 187272006033 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 187272006034 Putative water exit pathway; other site 187272006035 Binuclear center (active site) [active] 187272006036 Putative proton exit pathway; other site 187272006037 MoxR-like ATPases [General function prediction only]; Region: COG0714 187272006038 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 187272006039 Walker A motif; other site 187272006040 ATP binding site [chemical binding]; other site 187272006041 Walker B motif; other site 187272006042 arginine finger; other site 187272006043 Protein of unknown function DUF58; Region: DUF58; pfam01882 187272006044 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 187272006045 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 187272006046 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 187272006047 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 187272006048 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_1; cd08581 187272006049 putative active site [active] 187272006050 catalytic site [active] 187272006051 putative metal binding site [ion binding]; other site 187272006052 Transcriptional regulator; Region: Rrf2; cl17282 187272006053 Rrf2 family protein; Region: rrf2_super; TIGR00738 187272006054 Protein of unknown function (DUF1249); Region: DUF1249; pfam06853 187272006055 PEP synthetase regulatory protein; Provisional; Region: PRK05339 187272006056 phosphoenolpyruvate synthase; Validated; Region: PRK06464 187272006057 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 187272006058 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 187272006059 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 187272006060 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 187272006061 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 187272006062 eyelet of channel; other site 187272006063 trimer interface [polypeptide binding]; other site 187272006064 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 187272006065 Flavodoxin; Region: Flavodoxin_1; pfam00258 187272006066 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 187272006067 FAD binding pocket [chemical binding]; other site 187272006068 conserved FAD binding motif [chemical binding]; other site 187272006069 phosphate binding motif [ion binding]; other site 187272006070 beta-alpha-beta structure motif; other site 187272006071 NAD binding pocket [chemical binding]; other site 187272006072 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 187272006073 FAD binding domain; Region: FAD_binding_4; pfam01565 187272006074 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 187272006075 FAD binding domain; Region: FAD_binding_4; pfam01565 187272006076 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 187272006077 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 187272006078 Cysteine-rich domain; Region: CCG; pfam02754 187272006079 Cysteine-rich domain; Region: CCG; pfam02754 187272006080 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 187272006081 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 187272006082 active site residue [active] 187272006083 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 187272006084 active site residue [active] 187272006085 dihydrodipicolinate reductase; Provisional; Region: PRK00048 187272006086 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 187272006087 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 187272006088 chaperone protein DnaJ; Provisional; Region: PRK10767 187272006089 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 187272006090 HSP70 interaction site [polypeptide binding]; other site 187272006091 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 187272006092 substrate binding site [polypeptide binding]; other site 187272006093 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 187272006094 Zn binding sites [ion binding]; other site 187272006095 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 187272006096 dimer interface [polypeptide binding]; other site 187272006097 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 187272006098 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 187272006099 nucleotide binding site [chemical binding]; other site 187272006100 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 187272006101 dimer interface [polypeptide binding]; other site 187272006102 GrpE; Region: GrpE; pfam01025 187272006103 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 187272006104 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 187272006105 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 187272006106 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01231 187272006107 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 187272006108 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 187272006109 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 187272006110 Walker A/P-loop; other site 187272006111 ATP binding site [chemical binding]; other site 187272006112 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 187272006113 Q-loop/lid; other site 187272006114 ABC transporter signature motif; other site 187272006115 Walker B; other site 187272006116 D-loop; other site 187272006117 H-loop/switch region; other site 187272006118 ferric uptake regulator; Provisional; Region: fur; PRK09462 187272006119 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 187272006120 metal binding site 2 [ion binding]; metal-binding site 187272006121 putative DNA binding helix; other site 187272006122 metal binding site 1 [ion binding]; metal-binding site 187272006123 dimer interface [polypeptide binding]; other site 187272006124 structural Zn2+ binding site [ion binding]; other site 187272006125 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 187272006126 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 187272006127 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 187272006128 hypothetical protein; Validated; Region: PRK01777 187272006129 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 187272006130 putative coenzyme Q binding site [chemical binding]; other site 187272006131 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 187272006132 SmpB-tmRNA interface; other site 187272006133 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 187272006134 Methyltransferase domain; Region: Methyltransf_31; pfam13847 187272006135 S-adenosylmethionine binding site [chemical binding]; other site 187272006136 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 187272006137 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 187272006138 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 187272006139 metal binding site [ion binding]; metal-binding site 187272006140 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 187272006141 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 187272006142 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 187272006143 EamA-like transporter family; Region: EamA; cl17759 187272006144 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 187272006145 EamA-like transporter family; Region: EamA; pfam00892 187272006146 Amidase; Region: Amidase; cl11426 187272006147 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 187272006148 Transcriptional regulators [Transcription]; Region: MarR; COG1846 187272006149 MarR family; Region: MarR_2; pfam12802 187272006150 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272006151 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 187272006152 Walker A/P-loop; other site 187272006153 ATP binding site [chemical binding]; other site 187272006154 Q-loop/lid; other site 187272006155 ABC transporter signature motif; other site 187272006156 Walker B; other site 187272006157 D-loop; other site 187272006158 H-loop/switch region; other site 187272006159 TOBE domain; Region: TOBE_2; pfam08402 187272006160 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 187272006161 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 187272006162 dimer interface [polypeptide binding]; other site 187272006163 conserved gate region; other site 187272006164 putative PBP binding loops; other site 187272006165 ABC-ATPase subunit interface; other site 187272006166 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 187272006167 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 187272006168 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 187272006169 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 187272006170 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 187272006171 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 187272006172 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 187272006173 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 187272006174 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272006175 GAF domain; Region: GAF; pfam01590 187272006176 PAS domain S-box; Region: sensory_box; TIGR00229 187272006177 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 187272006178 putative active site [active] 187272006179 heme pocket [chemical binding]; other site 187272006180 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272006181 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272006182 metal binding site [ion binding]; metal-binding site 187272006183 active site 187272006184 I-site; other site 187272006185 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 187272006186 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 187272006187 DGC domain; Region: DGC; pfam08859 187272006188 NnrS protein; Region: NnrS; cl01258 187272006189 NnrS protein; Region: NnrS; cl01258 187272006190 putative glutathione S-transferase; Provisional; Region: PRK10357 187272006191 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 187272006192 putative C-terminal domain interface [polypeptide binding]; other site 187272006193 putative GSH binding site (G-site) [chemical binding]; other site 187272006194 putative dimer interface [polypeptide binding]; other site 187272006195 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 187272006196 N-terminal domain interface [polypeptide binding]; other site 187272006197 dimer interface [polypeptide binding]; other site 187272006198 substrate binding pocket (H-site) [chemical binding]; other site 187272006199 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 187272006200 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 187272006201 transmembrane helices; other site 187272006202 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 187272006203 dimerization interface [polypeptide binding]; other site 187272006204 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 187272006205 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 187272006206 dimer interface [polypeptide binding]; other site 187272006207 putative CheW interface [polypeptide binding]; other site 187272006208 signal recognition particle protein; Provisional; Region: PRK10867 187272006209 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 187272006210 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 187272006211 P loop; other site 187272006212 GTP binding site [chemical binding]; other site 187272006213 Signal peptide binding domain; Region: SRP_SPB; pfam02978 187272006214 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 187272006215 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 187272006216 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 187272006217 putative catalytic residue [active] 187272006218 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 187272006219 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 187272006220 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 187272006221 DctM-like transporters; Region: DctM; pfam06808 187272006222 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 187272006223 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 187272006224 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 187272006225 RNase E interface [polypeptide binding]; other site 187272006226 trimer interface [polypeptide binding]; other site 187272006227 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 187272006228 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 187272006229 RNase E interface [polypeptide binding]; other site 187272006230 trimer interface [polypeptide binding]; other site 187272006231 active site 187272006232 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 187272006233 putative nucleic acid binding region [nucleotide binding]; other site 187272006234 G-X-X-G motif; other site 187272006235 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 187272006236 RNA binding site [nucleotide binding]; other site 187272006237 domain interface; other site 187272006238 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 187272006239 16S/18S rRNA binding site [nucleotide binding]; other site 187272006240 S13e-L30e interaction site [polypeptide binding]; other site 187272006241 25S rRNA binding site [nucleotide binding]; other site 187272006242 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 187272006243 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 187272006244 RNA binding site [nucleotide binding]; other site 187272006245 active site 187272006246 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 187272006247 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 187272006248 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 187272006249 translation initiation factor IF-2; Region: IF-2; TIGR00487 187272006250 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 187272006251 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 187272006252 G1 box; other site 187272006253 putative GEF interaction site [polypeptide binding]; other site 187272006254 GTP/Mg2+ binding site [chemical binding]; other site 187272006255 Switch I region; other site 187272006256 G2 box; other site 187272006257 G3 box; other site 187272006258 Switch II region; other site 187272006259 G4 box; other site 187272006260 G5 box; other site 187272006261 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 187272006262 Translation-initiation factor 2; Region: IF-2; pfam11987 187272006263 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 187272006264 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 187272006265 NusA N-terminal domain; Region: NusA_N; pfam08529 187272006266 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 187272006267 RNA binding site [nucleotide binding]; other site 187272006268 homodimer interface [polypeptide binding]; other site 187272006269 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 187272006270 G-X-X-G motif; other site 187272006271 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 187272006272 G-X-X-G motif; other site 187272006273 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 187272006274 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 187272006275 ribosome maturation protein RimP; Reviewed; Region: PRK00092 187272006276 Sm and related proteins; Region: Sm_like; cl00259 187272006277 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 187272006278 putative oligomer interface [polypeptide binding]; other site 187272006279 putative RNA binding site [nucleotide binding]; other site 187272006280 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 187272006281 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 187272006282 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 187272006283 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 187272006284 S-adenosylmethionine binding site [chemical binding]; other site 187272006285 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 187272006286 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 187272006287 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 187272006288 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 187272006289 active site 187272006290 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 187272006291 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 187272006292 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272006293 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 187272006294 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272006295 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 187272006296 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 187272006297 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272006298 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 187272006299 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 187272006300 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 187272006301 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 187272006302 4Fe-4S binding domain; Region: Fer4; cl02805 187272006303 4Fe-4S binding domain; Region: Fer4; pfam00037 187272006304 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 187272006305 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 187272006306 NADH dehydrogenase subunit G; Validated; Region: PRK09129 187272006307 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 187272006308 catalytic loop [active] 187272006309 iron binding site [ion binding]; other site 187272006310 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 187272006311 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 187272006312 molybdopterin cofactor binding site; other site 187272006313 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 187272006314 molybdopterin cofactor binding site; other site 187272006315 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 187272006316 SLBB domain; Region: SLBB; pfam10531 187272006317 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 187272006318 NADH dehydrogenase subunit E; Validated; Region: PRK07539 187272006319 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 187272006320 putative dimer interface [polypeptide binding]; other site 187272006321 [2Fe-2S] cluster binding site [ion binding]; other site 187272006322 NADH dehydrogenase subunit D; Validated; Region: PRK06075 187272006323 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 187272006324 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 187272006325 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 187272006326 NADH dehydrogenase subunit B; Validated; Region: PRK06411 187272006327 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 187272006328 Preprotein translocase SecG subunit; Region: SecG; pfam03840 187272006329 triosephosphate isomerase; Provisional; Region: PRK14567 187272006330 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 187272006331 substrate binding site [chemical binding]; other site 187272006332 dimer interface [polypeptide binding]; other site 187272006333 catalytic triad [active] 187272006334 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 187272006335 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 187272006336 active site 187272006337 substrate binding site [chemical binding]; other site 187272006338 metal binding site [ion binding]; metal-binding site 187272006339 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 187272006340 dihydropteroate synthase; Region: DHPS; TIGR01496 187272006341 substrate binding pocket [chemical binding]; other site 187272006342 dimer interface [polypeptide binding]; other site 187272006343 inhibitor binding site; inhibition site 187272006344 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 187272006345 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 187272006346 Walker A motif; other site 187272006347 ATP binding site [chemical binding]; other site 187272006348 Walker B motif; other site 187272006349 arginine finger; other site 187272006350 Peptidase family M41; Region: Peptidase_M41; pfam01434 187272006351 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 187272006352 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 187272006353 S-adenosylmethionine binding site [chemical binding]; other site 187272006354 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 187272006355 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 187272006356 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 187272006357 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 187272006358 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 187272006359 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 187272006360 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 187272006361 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 187272006362 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 187272006363 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 187272006364 ATP-grasp domain; Region: ATP-grasp_4; cl17255 187272006365 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 187272006366 IMP binding site; other site 187272006367 dimer interface [polypeptide binding]; other site 187272006368 interdomain contacts; other site 187272006369 partial ornithine binding site; other site 187272006370 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 187272006371 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 187272006372 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 187272006373 catalytic site [active] 187272006374 subunit interface [polypeptide binding]; other site 187272006375 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 187272006376 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272006377 Walker A/P-loop; other site 187272006378 ATP binding site [chemical binding]; other site 187272006379 Q-loop/lid; other site 187272006380 ABC transporter signature motif; other site 187272006381 Walker B; other site 187272006382 D-loop; other site 187272006383 H-loop/switch region; other site 187272006384 inner membrane transport permease; Provisional; Region: PRK15066 187272006385 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 187272006386 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 187272006387 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 187272006388 active site 187272006389 H-NS histone family; Region: Histone_HNS; pfam00816 187272006390 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 187272006391 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 187272006392 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 187272006393 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 187272006394 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 187272006395 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 187272006396 dimer interface [polypeptide binding]; other site 187272006397 active site residues [active] 187272006398 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 187272006399 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 187272006400 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 187272006401 motif II; other site 187272006402 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 187272006403 active site 187272006404 catalytic site [active] 187272006405 substrate binding site [chemical binding]; other site 187272006406 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 187272006407 RNA/DNA hybrid binding site [nucleotide binding]; other site 187272006408 active site 187272006409 Methyltransferase domain; Region: Methyltransf_11; pfam08241 187272006410 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 187272006411 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 187272006412 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272006413 catalytic residue [active] 187272006414 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272006415 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 187272006416 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272006417 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272006418 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 187272006419 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 187272006420 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 187272006421 Switch I; other site 187272006422 Switch II; other site 187272006423 septum site-determining protein MinC; Region: minC; TIGR01222 187272006424 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 187272006425 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 187272006426 Predicted transcriptional regulator [Transcription]; Region: COG2932 187272006427 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 187272006428 Catalytic site [active] 187272006429 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 187272006430 TPR motif; other site 187272006431 TPR repeat; Region: TPR_11; pfam13414 187272006432 binding surface 187272006433 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 187272006434 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 187272006435 Na binding site [ion binding]; other site 187272006436 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 187272006437 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 187272006438 ligand binding site [chemical binding]; other site 187272006439 flexible hinge region; other site 187272006440 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 187272006441 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272006442 metal binding triad; other site 187272006443 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272006444 metal binding triad; other site 187272006445 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 187272006446 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 187272006447 PAS domain; Region: PAS_9; pfam13426 187272006448 putative active site [active] 187272006449 heme pocket [chemical binding]; other site 187272006450 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 187272006451 active site 187272006452 catalytic site [active] 187272006453 substrate binding site [chemical binding]; other site 187272006454 heat shock protein 90; Provisional; Region: PRK05218 187272006455 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272006456 ATP binding site [chemical binding]; other site 187272006457 Mg2+ binding site [ion binding]; other site 187272006458 G-X-G motif; other site 187272006459 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 187272006460 nickel responsive regulator; Provisional; Region: PRK02967 187272006461 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 187272006462 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 187272006463 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 187272006464 putative active site [active] 187272006465 heme pocket [chemical binding]; other site 187272006466 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 187272006467 dimer interface [polypeptide binding]; other site 187272006468 phosphorylation site [posttranslational modification] 187272006469 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272006470 ATP binding site [chemical binding]; other site 187272006471 Mg2+ binding site [ion binding]; other site 187272006472 G-X-G motif; other site 187272006473 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 187272006474 hydrogenase 2 large subunit; Provisional; Region: PRK10467 187272006475 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 187272006476 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 187272006477 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272006478 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272006479 active site 187272006480 phosphorylation site [posttranslational modification] 187272006481 intermolecular recognition site; other site 187272006482 dimerization interface [polypeptide binding]; other site 187272006483 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 187272006484 Walker A motif; other site 187272006485 ATP binding site [chemical binding]; other site 187272006486 Walker B motif; other site 187272006487 arginine finger; other site 187272006488 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272006489 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 187272006490 putative active site [active] 187272006491 putative substrate binding site [chemical binding]; other site 187272006492 putative cosubstrate binding site; other site 187272006493 catalytic site [active] 187272006494 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 187272006495 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 187272006496 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 187272006497 substrate binding site [chemical binding]; other site 187272006498 oxyanion hole (OAH) forming residues; other site 187272006499 trimer interface [polypeptide binding]; other site 187272006500 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 187272006501 dimerization interface [polypeptide binding]; other site 187272006502 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 187272006503 ATP binding site [chemical binding]; other site 187272006504 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 187272006505 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 187272006506 HupF/HypC family; Region: HupF_HypC; pfam01455 187272006507 Acylphosphatase; Region: Acylphosphatase; pfam00708 187272006508 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 187272006509 HypF finger; Region: zf-HYPF; pfam07503 187272006510 HypF finger; Region: zf-HYPF; pfam07503 187272006511 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 187272006512 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 187272006513 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 187272006514 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 187272006515 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 187272006516 [NiFe] hydrogenase assembly chaperone, HybE family; Region: hydrog_HybE; TIGR03993 187272006517 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 187272006518 Rubredoxin; Region: Rubredoxin; pfam00301 187272006519 iron binding site [ion binding]; other site 187272006520 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 187272006521 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 187272006522 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 187272006523 HupF/HypC family; Region: HupF_HypC; pfam01455 187272006524 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 187272006525 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 187272006526 putative substrate-binding site; other site 187272006527 nickel binding site [ion binding]; other site 187272006528 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 187272006529 hydrogenase 1 large subunit; Provisional; Region: PRK10170 187272006530 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 187272006531 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 187272006532 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 187272006533 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 187272006534 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 187272006535 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 187272006536 N-terminal plug; other site 187272006537 ligand-binding site [chemical binding]; other site 187272006538 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 187272006539 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 187272006540 ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]; Region: CbiM; cl00397 187272006541 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 187272006542 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 187272006543 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 187272006544 Walker A/P-loop; other site 187272006545 ATP binding site [chemical binding]; other site 187272006546 Q-loop/lid; other site 187272006547 ABC transporter signature motif; other site 187272006548 Walker B; other site 187272006549 D-loop; other site 187272006550 H-loop/switch region; other site 187272006551 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 187272006552 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 187272006553 DNA binding site [nucleotide binding] 187272006554 active site 187272006555 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 187272006556 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 187272006557 PYR/PP interface [polypeptide binding]; other site 187272006558 dimer interface [polypeptide binding]; other site 187272006559 TPP binding site [chemical binding]; other site 187272006560 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 187272006561 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 187272006562 TPP-binding site [chemical binding]; other site 187272006563 dimer interface [polypeptide binding]; other site 187272006564 methionine sulfoxide reductase B; Provisional; Region: PRK00222 187272006565 SelR domain; Region: SelR; pfam01641 187272006566 NAD-dependent deacetylase; Provisional; Region: PRK00481 187272006567 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 187272006568 NAD+ binding site [chemical binding]; other site 187272006569 substrate binding site [chemical binding]; other site 187272006570 Zn binding site [ion binding]; other site 187272006571 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 187272006572 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 187272006573 phosphoserine phosphatase SerB; Region: serB; TIGR00338 187272006574 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 187272006575 motif II; other site 187272006576 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 187272006577 PAS fold; Region: PAS_4; pfam08448 187272006578 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 187272006579 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 187272006580 Walker A motif; other site 187272006581 ATP binding site [chemical binding]; other site 187272006582 Walker B motif; other site 187272006583 arginine finger; other site 187272006584 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272006585 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 187272006586 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 187272006587 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 187272006588 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 187272006589 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 187272006590 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 187272006591 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 187272006592 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII; cd09992 187272006593 active site 187272006594 Zn binding site [ion binding]; other site 187272006595 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272006596 metal binding triad; other site 187272006597 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 187272006598 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 187272006599 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 187272006600 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 187272006601 Na binding site [ion binding]; other site 187272006602 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 187272006603 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 187272006604 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 187272006605 ligand binding site [chemical binding]; other site 187272006606 flexible hinge region; other site 187272006607 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 187272006608 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272006609 metal binding triad; other site 187272006610 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 187272006611 PAS domain; Region: PAS_9; pfam13426 187272006612 putative active site [active] 187272006613 heme pocket [chemical binding]; other site 187272006614 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 187272006615 active site 187272006616 catalytic site [active] 187272006617 substrate binding site [chemical binding]; other site 187272006618 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 187272006619 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272006620 active site 187272006621 phosphorylation site [posttranslational modification] 187272006622 intermolecular recognition site; other site 187272006623 dimerization interface [polypeptide binding]; other site 187272006624 FOG: CBS domain [General function prediction only]; Region: COG0517 187272006625 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272006626 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272006627 metal binding triad; other site 187272006628 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 187272006629 Proline racemase; Region: Pro_racemase; pfam05544 187272006630 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 187272006631 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR9; cd08274 187272006632 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 187272006633 putative NAD(P) binding site [chemical binding]; other site 187272006634 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 187272006635 Mechanosensitive ion channel; Region: MS_channel; pfam00924 187272006636 AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two...; Region: PurM-like1; cd06061 187272006637 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypE; COG0309 187272006638 dimerization interface [polypeptide binding]; other site 187272006639 putative ATP binding site [chemical binding]; other site 187272006640 NMT1-like family; Region: NMT1_2; pfam13379 187272006641 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 187272006642 homodimer interaction site [polypeptide binding]; other site 187272006643 cofactor binding site; other site 187272006644 PAS domain; Region: PAS; smart00091 187272006645 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272006646 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272006647 metal binding site [ion binding]; metal-binding site 187272006648 active site 187272006649 I-site; other site 187272006650 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 187272006651 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 187272006652 thiamine phosphate binding site [chemical binding]; other site 187272006653 active site 187272006654 pyrophosphate binding site [ion binding]; other site 187272006655 Rubredoxin [Energy production and conversion]; Region: COG1773 187272006656 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 187272006657 iron binding site [ion binding]; other site 187272006658 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 187272006659 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 187272006660 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 187272006661 ATP binding site [chemical binding]; other site 187272006662 Mg++ binding site [ion binding]; other site 187272006663 motif III; other site 187272006664 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 187272006665 nucleotide binding region [chemical binding]; other site 187272006666 ATP-binding site [chemical binding]; other site 187272006667 Protein of unknown function, DUF479; Region: DUF479; cl01203 187272006668 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 187272006669 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 187272006670 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 187272006671 DctM-like transporters; Region: DctM; pfam06808 187272006672 FOG: CBS domain [General function prediction only]; Region: COG0517 187272006673 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 187272006674 flagellar motor protein MotA; Validated; Region: PRK08124 187272006675 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 187272006676 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272006677 ligand binding site [chemical binding]; other site 187272006678 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272006679 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272006680 metal binding site [ion binding]; metal-binding site 187272006681 active site 187272006682 I-site; other site 187272006683 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 187272006684 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 187272006685 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 187272006686 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 187272006687 Walker A motif; other site 187272006688 ATP binding site [chemical binding]; other site 187272006689 Walker B motif; other site 187272006690 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 187272006691 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272006692 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272006693 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 187272006694 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 187272006695 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 187272006696 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 187272006697 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 187272006698 CoA-binding site [chemical binding]; other site 187272006699 ATP-binding [chemical binding]; other site 187272006700 hypothetical protein; Provisional; Region: PRK05287 187272006701 hypothetical protein; Provisional; Region: PRK08999 187272006702 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 187272006703 active site 187272006704 8-oxo-dGMP binding site [chemical binding]; other site 187272006705 nudix motif; other site 187272006706 metal binding site [ion binding]; metal-binding site 187272006707 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 187272006708 thiamine phosphate binding site [chemical binding]; other site 187272006709 active site 187272006710 pyrophosphate binding site [ion binding]; other site 187272006711 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 187272006712 heterotetramer interface [polypeptide binding]; other site 187272006713 active site pocket [active] 187272006714 cleavage site 187272006715 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 187272006716 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 187272006717 ATP binding site [chemical binding]; other site 187272006718 putative Mg++ binding site [ion binding]; other site 187272006719 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 187272006720 SEC-C motif; Region: SEC-C; pfam02810 187272006721 Protein of unknown function (DUF721); Region: DUF721; pfam05258 187272006722 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 187272006723 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 187272006724 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 187272006725 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 187272006726 putative active site; other site 187272006727 catalytic residue [active] 187272006728 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12647 187272006729 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272006730 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 187272006731 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12509 187272006732 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK12659 187272006733 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12663 187272006734 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 187272006735 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 187272006736 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 187272006737 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 187272006738 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05742 187272006739 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 187272006740 dimerization interface [polypeptide binding]; other site 187272006741 active site 187272006742 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 187272006743 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272006744 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272006745 ABC transporter; Region: ABC_tran_2; pfam12848 187272006746 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272006747 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 187272006748 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 187272006749 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 187272006750 putative active site [active] 187272006751 putative substrate binding site [chemical binding]; other site 187272006752 putative cosubstrate binding site; other site 187272006753 catalytic site [active] 187272006754 Sporulation related domain; Region: SPOR; cl10051 187272006755 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 187272006756 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 187272006757 homodimer interface [polypeptide binding]; other site 187272006758 substrate-cofactor binding pocket; other site 187272006759 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272006760 catalytic residue [active] 187272006761 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 187272006762 ATP cone domain; Region: ATP-cone; pfam03477 187272006763 ATP cone domain; Region: ATP-cone; pfam03477 187272006764 Class I ribonucleotide reductase; Region: RNR_I; cd01679 187272006765 active site 187272006766 dimer interface [polypeptide binding]; other site 187272006767 catalytic residues [active] 187272006768 effector binding site; other site 187272006769 R2 peptide binding site; other site 187272006770 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 187272006771 dimer interface [polypeptide binding]; other site 187272006772 putative radical transfer pathway; other site 187272006773 diiron center [ion binding]; other site 187272006774 tyrosyl radical; other site 187272006775 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 187272006776 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272006777 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 187272006778 putative dimerization interface [polypeptide binding]; other site 187272006779 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 187272006780 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 187272006781 THF binding site; other site 187272006782 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 187272006783 substrate binding site [chemical binding]; other site 187272006784 THF binding site; other site 187272006785 zinc-binding site [ion binding]; other site 187272006786 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 187272006787 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 187272006788 acyl-activating enzyme (AAE) consensus motif; other site 187272006789 putative AMP binding site [chemical binding]; other site 187272006790 putative active site [active] 187272006791 putative CoA binding site [chemical binding]; other site 187272006792 short chain dehydrogenase; Provisional; Region: PRK08278 187272006793 human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs; Region: HSDL2_SDR_c; cd09762 187272006794 NAD(P) binding site [chemical binding]; other site 187272006795 homodimer interface [polypeptide binding]; other site 187272006796 active site 187272006797 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 187272006798 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 187272006799 dimer interface [polypeptide binding]; other site 187272006800 active site 187272006801 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 187272006802 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 187272006803 substrate binding site [chemical binding]; other site 187272006804 oxyanion hole (OAH) forming residues; other site 187272006805 trimer interface [polypeptide binding]; other site 187272006806 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 187272006807 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 187272006808 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 187272006809 active site 187272006810 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 187272006811 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 187272006812 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 187272006813 Active Sites [active] 187272006814 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 187272006815 Subunit I/III interface [polypeptide binding]; other site 187272006816 Cytochrome c; Region: Cytochrom_C; pfam00034 187272006817 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 187272006818 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 187272006819 Putative water exit pathway; other site 187272006820 Binuclear center (active site) [active] 187272006821 K-pathway; other site 187272006822 Putative proton exit pathway; other site 187272006823 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 187272006824 MoxR-like ATPases [General function prediction only]; Region: COG0714 187272006825 Walker A motif; other site 187272006826 ATP binding site [chemical binding]; other site 187272006827 Walker B motif; other site 187272006828 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 187272006829 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 187272006830 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 187272006831 metal ion-dependent adhesion site (MIDAS); other site 187272006832 Predicted membrane protein [Function unknown]; Region: COG3671 187272006833 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 187272006834 glutamate dehydrogenase; Provisional; Region: PRK09414 187272006835 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 187272006836 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 187272006837 NAD(P) binding site [chemical binding]; other site 187272006838 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 187272006839 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 187272006840 active site 187272006841 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 187272006842 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 187272006843 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 187272006844 dimer interface [polypeptide binding]; other site 187272006845 active site 187272006846 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 187272006847 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 187272006848 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 187272006849 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 187272006850 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 187272006851 substrate binding site [chemical binding]; other site 187272006852 oxyanion hole (OAH) forming residues; other site 187272006853 trimer interface [polypeptide binding]; other site 187272006854 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 187272006855 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 187272006856 acyl-activating enzyme (AAE) consensus motif; other site 187272006857 putative AMP binding site [chemical binding]; other site 187272006858 putative active site [active] 187272006859 putative CoA binding site [chemical binding]; other site 187272006860 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 187272006861 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 187272006862 active site 187272006863 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 187272006864 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 187272006865 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 187272006866 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 187272006867 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 187272006868 HSP70 interaction site [polypeptide binding]; other site 187272006869 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 187272006870 substrate binding site [polypeptide binding]; other site 187272006871 dimer interface [polypeptide binding]; other site 187272006872 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 187272006873 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 187272006874 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 187272006875 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 187272006876 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 187272006877 substrate binding pocket [chemical binding]; other site 187272006878 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 187272006879 B12 binding site [chemical binding]; other site 187272006880 cobalt ligand [ion binding]; other site 187272006881 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 187272006882 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 187272006883 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 187272006884 ligand binding site [chemical binding]; other site 187272006885 flexible hinge region; other site 187272006886 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 187272006887 non-specific DNA interactions [nucleotide binding]; other site 187272006888 DNA binding site [nucleotide binding] 187272006889 sequence specific DNA binding site [nucleotide binding]; other site 187272006890 putative cAMP binding site [chemical binding]; other site 187272006891 SCP-2 sterol transfer family; Region: SCP2; cl01225 187272006892 putative protease; Provisional; Region: PRK15447 187272006893 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 187272006894 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 187272006895 Peptidase family U32; Region: Peptidase_U32; pfam01136 187272006896 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 187272006897 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 187272006898 tetramer interface [polypeptide binding]; other site 187272006899 catalytic Zn binding site [ion binding]; other site 187272006900 NADP binding site [chemical binding]; other site 187272006901 Predicted membrane protein [Function unknown]; Region: COG3671 187272006902 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 187272006903 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 187272006904 Walker A/P-loop; other site 187272006905 ATP binding site [chemical binding]; other site 187272006906 Q-loop/lid; other site 187272006907 ABC transporter signature motif; other site 187272006908 Walker B; other site 187272006909 D-loop; other site 187272006910 H-loop/switch region; other site 187272006911 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 187272006912 dimer interface [polypeptide binding]; other site 187272006913 conserved gate region; other site 187272006914 putative PBP binding loops; other site 187272006915 ABC-ATPase subunit interface; other site 187272006916 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 187272006917 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 187272006918 substrate binding pocket [chemical binding]; other site 187272006919 membrane-bound complex binding site; other site 187272006920 hinge residues; other site 187272006921 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 187272006922 C factor cell-cell signaling protein; Provisional; Region: PRK09009 187272006923 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 187272006924 NADP binding site [chemical binding]; other site 187272006925 homodimer interface [polypeptide binding]; other site 187272006926 active site 187272006927 Outer membrane efflux protein; Region: OEP; pfam02321 187272006928 Outer membrane efflux protein; Region: OEP; pfam02321 187272006929 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 187272006930 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 187272006931 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272006932 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 187272006933 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 187272006934 Walker A/P-loop; other site 187272006935 ATP binding site [chemical binding]; other site 187272006936 Q-loop/lid; other site 187272006937 ABC transporter signature motif; other site 187272006938 Walker B; other site 187272006939 D-loop; other site 187272006940 H-loop/switch region; other site 187272006941 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 187272006942 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 187272006943 FtsX-like permease family; Region: FtsX; pfam02687 187272006944 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 187272006945 putative active site [active] 187272006946 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 187272006947 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272006948 active site 187272006949 phosphorylation site [posttranslational modification] 187272006950 intermolecular recognition site; other site 187272006951 dimerization interface [polypeptide binding]; other site 187272006952 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 187272006953 DNA binding residues [nucleotide binding] 187272006954 dimerization interface [polypeptide binding]; other site 187272006955 GAF domain; Region: GAF; cl17456 187272006956 PAS fold; Region: PAS_3; pfam08447 187272006957 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 187272006958 putative active site [active] 187272006959 heme pocket [chemical binding]; other site 187272006960 PAS domain S-box; Region: sensory_box; TIGR00229 187272006961 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 187272006962 putative active site [active] 187272006963 heme pocket [chemical binding]; other site 187272006964 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 187272006965 dimer interface [polypeptide binding]; other site 187272006966 phosphorylation site [posttranslational modification] 187272006967 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272006968 ATP binding site [chemical binding]; other site 187272006969 G-X-G motif; other site 187272006970 Response regulator receiver domain; Region: Response_reg; pfam00072 187272006971 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272006972 active site 187272006973 phosphorylation site [posttranslational modification] 187272006974 intermolecular recognition site; other site 187272006975 dimerization interface [polypeptide binding]; other site 187272006976 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 187272006977 Predicted membrane protein [Function unknown]; Region: COG4655 187272006978 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 187272006979 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 187272006980 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 187272006981 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 187272006982 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272006983 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 187272006984 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272006985 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 187272006986 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 187272006987 ATP binding site [chemical binding]; other site 187272006988 Walker A motif; other site 187272006989 hexamer interface [polypeptide binding]; other site 187272006990 Walker B motif; other site 187272006991 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 187272006992 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 187272006993 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 187272006994 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 187272006995 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 187272006996 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 187272006997 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 187272006998 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 187272006999 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 187272007000 E3 interaction surface; other site 187272007001 lipoyl attachment site [posttranslational modification]; other site 187272007002 HlyD family secretion protein; Region: HlyD_3; pfam13437 187272007003 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 187272007004 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272007005 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007006 Walker A/P-loop; other site 187272007007 ATP binding site [chemical binding]; other site 187272007008 Q-loop/lid; other site 187272007009 ABC transporter signature motif; other site 187272007010 Walker B; other site 187272007011 D-loop; other site 187272007012 H-loop/switch region; other site 187272007013 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 187272007014 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 187272007015 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272007016 ligand binding site [chemical binding]; other site 187272007017 Response regulator receiver domain; Region: Response_reg; pfam00072 187272007018 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 187272007019 active site 187272007020 phosphorylation site [posttranslational modification] 187272007021 intermolecular recognition site; other site 187272007022 dimerization interface [polypeptide binding]; other site 187272007023 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 187272007024 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 187272007025 N-acetyl-D-glucosamine binding site [chemical binding]; other site 187272007026 catalytic residue [active] 187272007027 Uncharacterized conserved protein [Function unknown]; Region: COG1739 187272007028 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 187272007029 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 187272007030 Alpha/beta hydrolase of unknown function (DUF900); Region: DUF900; pfam05990 187272007031 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 187272007032 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272007033 Walker A/P-loop; other site 187272007034 ATP binding site [chemical binding]; other site 187272007035 Q-loop/lid; other site 187272007036 ABC transporter signature motif; other site 187272007037 Walker B; other site 187272007038 D-loop; other site 187272007039 H-loop/switch region; other site 187272007040 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 187272007041 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 187272007042 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272007043 Walker A/P-loop; other site 187272007044 ATP binding site [chemical binding]; other site 187272007045 Q-loop/lid; other site 187272007046 ABC transporter signature motif; other site 187272007047 Walker B; other site 187272007048 D-loop; other site 187272007049 H-loop/switch region; other site 187272007050 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 187272007051 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 187272007052 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 187272007053 dimer interface [polypeptide binding]; other site 187272007054 conserved gate region; other site 187272007055 putative PBP binding loops; other site 187272007056 ABC-ATPase subunit interface; other site 187272007057 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 187272007058 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 187272007059 dimer interface [polypeptide binding]; other site 187272007060 conserved gate region; other site 187272007061 putative PBP binding loops; other site 187272007062 ABC-ATPase subunit interface; other site 187272007063 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 187272007064 Predicted solute binding protein [General function prediction only]; Region: COG3889 187272007065 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 187272007066 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 187272007067 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 187272007068 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272007069 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272007070 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007071 AAA domain; Region: AAA_21; pfam13304 187272007072 Walker A/P-loop; other site 187272007073 ATP binding site [chemical binding]; other site 187272007074 Q-loop/lid; other site 187272007075 ABC transporter signature motif; other site 187272007076 Walker B; other site 187272007077 D-loop; other site 187272007078 H-loop/switch region; other site 187272007079 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272007080 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272007081 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007082 Walker A/P-loop; other site 187272007083 ATP binding site [chemical binding]; other site 187272007084 Q-loop/lid; other site 187272007085 ABC transporter signature motif; other site 187272007086 Walker B; other site 187272007087 D-loop; other site 187272007088 H-loop/switch region; other site 187272007089 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 187272007090 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 187272007091 cell division protein FtsZ; Validated; Region: PRK09330 187272007092 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 187272007093 nucleotide binding site [chemical binding]; other site 187272007094 SulA interaction site; other site 187272007095 cell division protein FtsA; Region: ftsA; TIGR01174 187272007096 Cell division protein FtsA; Region: FtsA; smart00842 187272007097 Cell division protein FtsA; Region: FtsA; pfam14450 187272007098 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 187272007099 Cell division protein FtsQ; Region: FtsQ; pfam03799 187272007100 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 187272007101 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 187272007102 ATP-grasp domain; Region: ATP-grasp_4; cl17255 187272007103 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 187272007104 FAD binding domain; Region: FAD_binding_4; pfam01565 187272007105 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 187272007106 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 187272007107 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 187272007108 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272007109 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 187272007110 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 187272007111 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 187272007112 active site 187272007113 homodimer interface [polypeptide binding]; other site 187272007114 cell division protein FtsW; Region: ftsW; TIGR02614 187272007115 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 187272007116 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272007117 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 187272007118 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 187272007119 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 187272007120 Mg++ binding site [ion binding]; other site 187272007121 putative catalytic motif [active] 187272007122 putative substrate binding site [chemical binding]; other site 187272007123 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 187272007124 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 187272007125 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272007126 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 187272007127 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 187272007128 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 187272007129 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 187272007130 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 187272007131 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 187272007132 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 187272007133 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 187272007134 Cell division protein FtsL; Region: FtsL; pfam04999 187272007135 MraW methylase family; Region: Methyltransf_5; cl17771 187272007136 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 187272007137 cell division protein MraZ; Reviewed; Region: PRK00326 187272007138 MraZ protein; Region: MraZ; pfam02381 187272007139 MraZ protein; Region: MraZ; pfam02381 187272007140 Predicted methyltransferases [General function prediction only]; Region: COG0313 187272007141 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 187272007142 putative SAM binding site [chemical binding]; other site 187272007143 putative homodimer interface [polypeptide binding]; other site 187272007144 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 187272007145 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 187272007146 putative ligand binding site [chemical binding]; other site 187272007147 hypothetical protein; Reviewed; Region: PRK12497 187272007148 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 187272007149 dimer interface [polypeptide binding]; other site 187272007150 active site 187272007151 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 187272007152 stringent starvation protein A; Provisional; Region: sspA; PRK09481 187272007153 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 187272007154 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 187272007155 dimer interface [polypeptide binding]; other site 187272007156 N-terminal domain interface [polypeptide binding]; other site 187272007157 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 187272007158 cytochrome b; Provisional; Region: CYTB; MTH00145 187272007159 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 187272007160 Qi binding site; other site 187272007161 intrachain domain interface; other site 187272007162 interchain domain interface [polypeptide binding]; other site 187272007163 heme bH binding site [chemical binding]; other site 187272007164 heme bL binding site [chemical binding]; other site 187272007165 Qo binding site; other site 187272007166 interchain domain interface [polypeptide binding]; other site 187272007167 intrachain domain interface; other site 187272007168 Qi binding site; other site 187272007169 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 187272007170 Qo binding site; other site 187272007171 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 187272007172 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 187272007173 [2Fe-2S] cluster binding site [ion binding]; other site 187272007174 Uncharacterized conserved protein [Function unknown]; Region: COG0327 187272007175 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 187272007176 serine endoprotease; Provisional; Region: PRK10898 187272007177 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 187272007178 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 187272007179 protein binding site [polypeptide binding]; other site 187272007180 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 187272007181 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 187272007182 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272007183 homodimer interface [polypeptide binding]; other site 187272007184 catalytic residue [active] 187272007185 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 187272007186 histidinol dehydrogenase; Region: hisD; TIGR00069 187272007187 NAD binding site [chemical binding]; other site 187272007188 dimerization interface [polypeptide binding]; other site 187272007189 product binding site; other site 187272007190 substrate binding site [chemical binding]; other site 187272007191 zinc binding site [ion binding]; other site 187272007192 catalytic residues [active] 187272007193 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 187272007194 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 187272007195 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 187272007196 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 187272007197 hinge; other site 187272007198 active site 187272007199 BolA-like protein; Region: BolA; pfam01722 187272007200 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 187272007201 anti sigma factor interaction site; other site 187272007202 regulatory phosphorylation site [posttranslational modification]; other site 187272007203 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 187272007204 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 187272007205 mce related protein; Region: MCE; pfam02470 187272007206 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 187272007207 Permease; Region: Permease; pfam02405 187272007208 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 187272007209 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 187272007210 Walker A/P-loop; other site 187272007211 ATP binding site [chemical binding]; other site 187272007212 Q-loop/lid; other site 187272007213 ABC transporter signature motif; other site 187272007214 Walker B; other site 187272007215 D-loop; other site 187272007216 H-loop/switch region; other site 187272007217 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 187272007218 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 187272007219 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 187272007220 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 187272007221 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 187272007222 putative active site [active] 187272007223 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 187272007224 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 187272007225 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 187272007226 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 187272007227 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 187272007228 OstA-like protein; Region: OstA; pfam03968 187272007229 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 187272007230 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 187272007231 Walker A/P-loop; other site 187272007232 ATP binding site [chemical binding]; other site 187272007233 Q-loop/lid; other site 187272007234 ABC transporter signature motif; other site 187272007235 Walker B; other site 187272007236 D-loop; other site 187272007237 H-loop/switch region; other site 187272007238 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 187272007239 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 187272007240 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 187272007241 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 187272007242 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 187272007243 30S subunit binding site; other site 187272007244 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 187272007245 active site 187272007246 phosphorylation site [posttranslational modification] 187272007247 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 187272007248 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 187272007249 regulatory protein interface [polypeptide binding]; other site 187272007250 active site 187272007251 regulatory phosphorylation site [posttranslational modification]; other site 187272007252 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 187272007253 ATP-grasp domain; Region: ATP-grasp; pfam02222 187272007254 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 187272007255 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 187272007256 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 187272007257 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 187272007258 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 187272007259 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 187272007260 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 187272007261 23S rRNA interface [nucleotide binding]; other site 187272007262 L3 interface [polypeptide binding]; other site 187272007263 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 187272007264 dimer interface [polypeptide binding]; other site 187272007265 [2Fe-2S] cluster binding site [ion binding]; other site 187272007266 S-adenosylmethionine decarboxylase; Provisional; Region: PRK05462 187272007267 OsmC-like protein; Region: OsmC; cl00767 187272007268 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 187272007269 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 187272007270 ligand binding site [chemical binding]; other site 187272007271 flexible hinge region; other site 187272007272 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 187272007273 putative switch regulator; other site 187272007274 non-specific DNA interactions [nucleotide binding]; other site 187272007275 DNA binding site [nucleotide binding] 187272007276 sequence specific DNA binding site [nucleotide binding]; other site 187272007277 putative cAMP binding site [chemical binding]; other site 187272007278 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 187272007279 active site 187272007280 ribulose/triose binding site [chemical binding]; other site 187272007281 phosphate binding site [ion binding]; other site 187272007282 substrate (anthranilate) binding pocket [chemical binding]; other site 187272007283 product (indole) binding pocket [chemical binding]; other site 187272007284 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 187272007285 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 187272007286 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 187272007287 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 187272007288 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 187272007289 glutamine binding [chemical binding]; other site 187272007290 catalytic triad [active] 187272007291 anthranilate synthase component I; Provisional; Region: PRK13565 187272007292 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 187272007293 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 187272007294 phosphoglycolate phosphatase; Provisional; Region: PRK13222 187272007295 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 187272007296 motif II; other site 187272007297 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 187272007298 putative metal binding site [ion binding]; other site 187272007299 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 187272007300 HSP70 interaction site [polypeptide binding]; other site 187272007301 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 187272007302 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 187272007303 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 187272007304 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 187272007305 S-adenosylmethionine binding site [chemical binding]; other site 187272007306 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 187272007307 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 187272007308 DNA binding residues [nucleotide binding] 187272007309 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 187272007310 DNA photolyase; Region: DNA_photolyase; pfam00875 187272007311 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 187272007312 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 187272007313 ATP binding site [chemical binding]; other site 187272007314 active site 187272007315 substrate binding site [chemical binding]; other site 187272007316 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 187272007317 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 187272007318 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 187272007319 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 187272007320 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 187272007321 transketolase; Reviewed; Region: PRK12753 187272007322 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 187272007323 TPP-binding site [chemical binding]; other site 187272007324 dimer interface [polypeptide binding]; other site 187272007325 Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding...; Region: H2A; cl00074 187272007326 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 187272007327 PYR/PP interface [polypeptide binding]; other site 187272007328 dimer interface [polypeptide binding]; other site 187272007329 TPP binding site [chemical binding]; other site 187272007330 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 187272007331 S-adenosylmethionine synthetase; Validated; Region: PRK05250 187272007332 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 187272007333 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 187272007334 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 187272007335 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 187272007336 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 187272007337 homotetramer interface [polypeptide binding]; other site 187272007338 ligand binding site [chemical binding]; other site 187272007339 catalytic site [active] 187272007340 NAD binding site [chemical binding]; other site 187272007341 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 187272007342 FAD binding site [chemical binding]; other site 187272007343 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 187272007344 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 187272007345 ATP-grasp domain; Region: ATP-grasp_4; cl17255 187272007346 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 187272007347 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 187272007348 dimer interface [polypeptide binding]; other site 187272007349 catalytic site [active] 187272007350 putative active site [active] 187272007351 putative substrate binding site [chemical binding]; other site 187272007352 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 187272007353 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272007354 Walker A/P-loop; other site 187272007355 ATP binding site [chemical binding]; other site 187272007356 Q-loop/lid; other site 187272007357 ABC transporter signature motif; other site 187272007358 Walker B; other site 187272007359 D-loop; other site 187272007360 H-loop/switch region; other site 187272007361 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 187272007362 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 187272007363 Walker A/P-loop; other site 187272007364 ATP binding site [chemical binding]; other site 187272007365 Q-loop/lid; other site 187272007366 ABC transporter signature motif; other site 187272007367 Walker B; other site 187272007368 D-loop; other site 187272007369 H-loop/switch region; other site 187272007370 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 187272007371 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 187272007372 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 187272007373 dimer interface [polypeptide binding]; other site 187272007374 conserved gate region; other site 187272007375 putative PBP binding loops; other site 187272007376 ABC-ATPase subunit interface; other site 187272007377 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 187272007378 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 187272007379 dimer interface [polypeptide binding]; other site 187272007380 conserved gate region; other site 187272007381 putative PBP binding loops; other site 187272007382 ABC-ATPase subunit interface; other site 187272007383 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 187272007384 YcfA-like protein; Region: YcfA; pfam07927 187272007385 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 187272007386 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 187272007387 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 187272007388 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 187272007389 N-terminal plug; other site 187272007390 ligand-binding site [chemical binding]; other site 187272007391 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 187272007392 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 187272007393 NAD binding site [chemical binding]; other site 187272007394 homotetramer interface [polypeptide binding]; other site 187272007395 homodimer interface [polypeptide binding]; other site 187272007396 substrate binding site [chemical binding]; other site 187272007397 active site 187272007398 Protein of unknown function (DUF3568); Region: DUF3568; pfam12092 187272007399 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 187272007400 L-lactate permease; Region: Lactate_perm; cl00701 187272007401 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 187272007402 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 187272007403 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 187272007404 4Fe-4S binding domain; Region: Fer4; pfam00037 187272007405 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 187272007406 Cysteine-rich domain; Region: CCG; pfam02754 187272007407 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 187272007408 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 187272007409 DNA-binding site [nucleotide binding]; DNA binding site 187272007410 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 187272007411 SurA N-terminal domain; Region: SurA_N_3; cl07813 187272007412 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 187272007413 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 187272007414 IHF dimer interface [polypeptide binding]; other site 187272007415 IHF - DNA interface [nucleotide binding]; other site 187272007416 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 187272007417 Found in ATP-dependent protease La (LON); Region: LON; smart00464 187272007418 Found in ATP-dependent protease La (LON); Region: LON; smart00464 187272007419 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 187272007420 Walker A motif; other site 187272007421 ATP binding site [chemical binding]; other site 187272007422 Walker B motif; other site 187272007423 arginine finger; other site 187272007424 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 187272007425 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 187272007426 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 187272007427 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 187272007428 Walker A motif; other site 187272007429 ATP binding site [chemical binding]; other site 187272007430 Walker B motif; other site 187272007431 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 187272007432 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 187272007433 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 187272007434 oligomer interface [polypeptide binding]; other site 187272007435 active site residues [active] 187272007436 trigger factor; Provisional; Region: tig; PRK01490 187272007437 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 187272007438 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 187272007439 Uncharacterized conserved protein [Function unknown]; Region: COG1434 187272007440 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 187272007441 putative active site [active] 187272007442 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 187272007443 GIY-YIG motif/motif A; other site 187272007444 putative active site [active] 187272007445 putative metal binding site [ion binding]; other site 187272007446 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4924 187272007447 Uncharacterized protein conserved in bacteria N-term (DUF3322); Region: DUF3322; pfam11795 187272007448 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 187272007449 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 187272007450 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 187272007451 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 187272007452 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 187272007453 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 187272007454 Divergent AAA domain; Region: AAA_4; pfam04326 187272007455 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 187272007456 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 187272007457 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 187272007458 P-loop; other site 187272007459 Magnesium ion binding site [ion binding]; other site 187272007460 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 187272007461 Magnesium ion binding site [ion binding]; other site 187272007462 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 187272007463 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 187272007464 non-specific DNA binding site [nucleotide binding]; other site 187272007465 salt bridge; other site 187272007466 sequence-specific DNA binding site [nucleotide binding]; other site 187272007467 HipA N-terminal domain; Region: Couple_hipA; pfam13657 187272007468 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 187272007469 HipA-like N-terminal domain; Region: HipA_N; pfam07805 187272007470 HipA-like C-terminal domain; Region: HipA_C; pfam07804 187272007471 PIN domain; Region: PIN_3; pfam13470 187272007472 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 187272007473 YgiT-type zinc finger domain; Region: YgiT_finger; TIGR03831 187272007474 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 187272007475 non-specific DNA binding site [nucleotide binding]; other site 187272007476 salt bridge; other site 187272007477 sequence-specific DNA binding site [nucleotide binding]; other site 187272007478 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 187272007479 Preprotein binding site; other site 187272007480 SecA binding site; other site 187272007481 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 187272007482 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 187272007483 Beta-Casp domain; Region: Beta-Casp; smart01027 187272007484 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 187272007485 Predicted ATPase [General function prediction only]; Region: COG4637 187272007486 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007487 Walker A/P-loop; other site 187272007488 ATP binding site [chemical binding]; other site 187272007489 Q-loop/lid; other site 187272007490 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007491 Walker B; other site 187272007492 D-loop; other site 187272007493 H-loop/switch region; other site 187272007494 Domain of unknown function (DUF4276); Region: DUF4276; pfam14103 187272007495 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 187272007496 putative DNA binding site [nucleotide binding]; other site 187272007497 putative Zn2+ binding site [ion binding]; other site 187272007498 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 187272007499 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 187272007500 NAD binding site [chemical binding]; other site 187272007501 substrate binding site [chemical binding]; other site 187272007502 homodimer interface [polypeptide binding]; other site 187272007503 active site 187272007504 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 187272007505 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 187272007506 NADP binding site [chemical binding]; other site 187272007507 active site 187272007508 putative substrate binding site [chemical binding]; other site 187272007509 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 187272007510 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 187272007511 substrate binding site; other site 187272007512 tetramer interface; other site 187272007513 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 187272007514 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 187272007515 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272007516 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007517 Walker A/P-loop; other site 187272007518 ATP binding site [chemical binding]; other site 187272007519 Q-loop/lid; other site 187272007520 ABC transporter signature motif; other site 187272007521 Walker B; other site 187272007522 D-loop; other site 187272007523 H-loop/switch region; other site 187272007524 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 187272007525 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 187272007526 NAD(P) binding site [chemical binding]; other site 187272007527 homodimer interface [polypeptide binding]; other site 187272007528 substrate binding site [chemical binding]; other site 187272007529 active site 187272007530 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 187272007531 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 187272007532 inhibitor-cofactor binding pocket; inhibition site 187272007533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272007534 catalytic residue [active] 187272007535 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 187272007536 ligand binding site; other site 187272007537 tetramer interface; other site 187272007538 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 187272007539 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 187272007540 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 187272007541 pseudaminic acid synthase; Region: PseI; TIGR03586 187272007542 NeuB family; Region: NeuB; pfam03102 187272007543 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 187272007544 NeuB binding interface [polypeptide binding]; other site 187272007545 putative substrate binding site [chemical binding]; other site 187272007546 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 187272007547 Winged helix-turn helix; Region: HTH_29; pfam13551 187272007548 Integrase core domain; Region: rve; pfam00665 187272007549 DDE domain; Region: DDE_Tnp_IS240; pfam13610 187272007550 Integrase core domain; Region: rve_3; pfam13683 187272007551 Transposase; Region: HTH_Tnp_1; cl17663 187272007552 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272007553 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 187272007554 putative ADP-binding pocket [chemical binding]; other site 187272007555 Transposase; Region: HTH_Tnp_1; cl17663 187272007556 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 187272007557 probable regulatory domain; Region: near_KaiC_dom; TIGR03879 187272007558 Integrase core domain; Region: rve; pfam00665 187272007559 Integrase core domain; Region: rve_3; cl15866 187272007560 Transposase; Region: HTH_Tnp_1; cl17663 187272007561 putative transposase OrfB; Reviewed; Region: PHA02517 187272007562 Integrase core domain; Region: rve; pfam00665 187272007563 Integrase core domain; Region: rve_3; pfam13683 187272007564 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 187272007565 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272007566 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 187272007567 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 187272007568 active site 187272007569 dimer interface [polypeptide binding]; other site 187272007570 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 187272007571 Ligand Binding Site [chemical binding]; other site 187272007572 Molecular Tunnel; other site 187272007573 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 187272007574 putative ADP-binding pocket [chemical binding]; other site 187272007575 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272007576 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 187272007577 Mg++ binding site [ion binding]; other site 187272007578 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 187272007579 putative catalytic motif [active] 187272007580 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 187272007581 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 187272007582 active site 187272007583 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 187272007584 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 187272007585 Active Sites [active] 187272007586 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 187272007587 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 187272007588 CysD dimerization site [polypeptide binding]; other site 187272007589 G1 box; other site 187272007590 putative GEF interaction site [polypeptide binding]; other site 187272007591 GTP/Mg2+ binding site [chemical binding]; other site 187272007592 Switch I region; other site 187272007593 G2 box; other site 187272007594 G3 box; other site 187272007595 Switch II region; other site 187272007596 G4 box; other site 187272007597 G5 box; other site 187272007598 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 187272007599 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 187272007600 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 187272007601 ligand-binding site [chemical binding]; other site 187272007602 AAA domain; Region: AAA_14; pfam13173 187272007603 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 187272007604 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 187272007605 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 187272007606 TrkA-C domain; Region: TrkA_C; pfam02080 187272007607 TrkA-C domain; Region: TrkA_C; pfam02080 187272007608 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 187272007609 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 187272007610 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 187272007611 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 187272007612 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 187272007613 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 187272007614 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272007615 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 187272007616 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 187272007617 active site 187272007618 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 187272007619 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 187272007620 active site 187272007621 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 187272007622 active site 187272007623 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272007624 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007625 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 187272007626 Walker A/P-loop; other site 187272007627 ATP binding site [chemical binding]; other site 187272007628 Q-loop/lid; other site 187272007629 ABC transporter signature motif; other site 187272007630 Walker B; other site 187272007631 D-loop; other site 187272007632 H-loop/switch region; other site 187272007633 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 187272007634 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 187272007635 FeS/SAM binding site; other site 187272007636 Predicted glycosyl transferase [General function prediction only]; Region: COG4671 187272007637 Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3; Region: Rieske_RO_Alpha_PhDO_like; cd03479 187272007638 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 187272007639 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 187272007640 alpha subunit interface [polypeptide binding]; other site 187272007641 active site 187272007642 substrate binding site [chemical binding]; other site 187272007643 Fe binding site [ion binding]; other site 187272007644 Methyltransferase domain; Region: Methyltransf_24; pfam13578 187272007645 Isochorismatase family; Region: Isochorismatase; pfam00857 187272007646 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 187272007647 catalytic triad [active] 187272007648 conserved cis-peptide bond; other site 187272007649 NAD(P)+ dependent aldehyde dehydrogenase family; Region: ALDH; cd07078 187272007650 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 187272007651 NAD(P) binding site [chemical binding]; other site 187272007652 catalytic residues [active] 187272007653 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 187272007654 HEXXH motif domain; Region: mod_HExxH; TIGR04267 187272007655 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 187272007656 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272007657 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 187272007658 active site 187272007659 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 187272007660 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 187272007661 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 187272007662 NeuB family; Region: NeuB; pfam03102 187272007663 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 187272007664 NeuB binding interface [polypeptide binding]; other site 187272007665 putative substrate binding site [chemical binding]; other site 187272007666 Protein of unknown function (DUF563); Region: DUF563; pfam04577 187272007667 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 187272007668 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 187272007669 active site 187272007670 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 187272007671 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 187272007672 Acetokinase family; Region: Acetate_kinase; cl17229 187272007673 propionate/acetate kinase; Provisional; Region: PRK12379 187272007674 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 187272007675 (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 187272007676 dimer interaction site [polypeptide binding]; other site 187272007677 substrate-binding tunnel; other site 187272007678 active site 187272007679 catalytic site [active] 187272007680 substrate binding site [chemical binding]; other site 187272007681 phosphate acetyltransferase; Provisional; Region: PRK11890 187272007682 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 187272007683 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 187272007684 NAD binding site [chemical binding]; other site 187272007685 homotetramer interface [polypeptide binding]; other site 187272007686 homodimer interface [polypeptide binding]; other site 187272007687 substrate binding site [chemical binding]; other site 187272007688 active site 187272007689 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 187272007690 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 187272007691 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 187272007692 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 187272007693 Mechanosensitive ion channel; Region: MS_channel; pfam00924 187272007694 Protein of unknown function (DUF432); Region: DUF432; cl01027 187272007695 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 187272007696 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 187272007697 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 187272007698 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 187272007699 GspL periplasmic domain; Region: GspL_C; cl14909 187272007700 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 187272007701 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 187272007702 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 187272007703 active site 187272007704 catalytic residues [active] 187272007705 type II secretion system protein J; Region: gspJ; TIGR01711 187272007706 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 187272007707 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 187272007708 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 187272007709 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 187272007710 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 187272007711 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 187272007712 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 187272007713 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272007714 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 187272007715 CAAX protease self-immunity; Region: Abi; cl00558 187272007716 calcium-activated chloride channel protein 1; Region: hCaCC; TIGR00868 187272007717 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 187272007718 metal ion-dependent adhesion site (MIDAS); other site 187272007719 Streptogramin lyase [Defense mechanisms]; Region: Vgb; COG4257 187272007720 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 187272007721 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 187272007722 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 187272007723 structural tetrad; other site 187272007724 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 187272007725 Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; Region: RGL4_M; cd10316 187272007726 type II secretion system protein E; Region: type_II_gspE; TIGR02533 187272007727 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 187272007728 Walker A motif; other site 187272007729 ATP binding site [chemical binding]; other site 187272007730 Walker B motif; other site 187272007731 type II secretion system protein D; Region: type_II_gspD; TIGR02517 187272007732 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 187272007733 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 187272007734 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 187272007735 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 187272007736 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 187272007737 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 187272007738 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 187272007739 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 187272007740 DNA-binding HTH domain-containing proteins [Transcription]; Region: CsgD; COG2771 187272007741 DNA binding residues [nucleotide binding] 187272007742 dimerization interface [polypeptide binding]; other site 187272007743 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 187272007744 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 187272007745 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 187272007746 Walker A/P-loop; other site 187272007747 ATP binding site [chemical binding]; other site 187272007748 Q-loop/lid; other site 187272007749 ABC transporter signature motif; other site 187272007750 Walker B; other site 187272007751 D-loop; other site 187272007752 H-loop/switch region; other site 187272007753 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 187272007754 active site 187272007755 catalytic triad [active] 187272007756 oxyanion hole [active] 187272007757 switch loop; other site 187272007758 Putative exonuclease, RdgC; Region: RdgC; pfam04381 187272007759 TspO/MBR family; Region: TspO_MBR; pfam03073 187272007760 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 187272007761 Fumarase C-terminus; Region: Fumerase_C; pfam05683 187272007762 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 187272007763 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 187272007764 ligand binding site [chemical binding]; other site 187272007765 flexible hinge region; other site 187272007766 HDOD domain; Region: HDOD; pfam08668 187272007767 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 187272007768 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 187272007769 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 187272007770 anti sigma factor interaction site; other site 187272007771 regulatory phosphorylation site [posttranslational modification]; other site 187272007772 Dodecin; Region: Dodecin; pfam07311 187272007773 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 187272007774 Isochorismatase family; Region: Isochorismatase; pfam00857 187272007775 catalytic triad [active] 187272007776 dimer interface [polypeptide binding]; other site 187272007777 conserved cis-peptide bond; other site 187272007778 Outer membrane lipoprotein Slp family; Region: Slp; pfam03843 187272007779 Outer membrane lipoprotein Slp family; Region: Slp; pfam03843 187272007780 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 187272007781 active site clefts [active] 187272007782 zinc binding site [ion binding]; other site 187272007783 dimer interface [polypeptide binding]; other site 187272007784 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 187272007785 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 187272007786 P-loop; other site 187272007787 Magnesium ion binding site [ion binding]; other site 187272007788 CHAD domain; Region: CHAD; pfam05235 187272007789 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 187272007790 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272007791 Walker A/P-loop; other site 187272007792 ATP binding site [chemical binding]; other site 187272007793 Q-loop/lid; other site 187272007794 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272007795 ABC transporter signature motif; other site 187272007796 Walker B; other site 187272007797 D-loop; other site 187272007798 ABC transporter; Region: ABC_tran_2; pfam12848 187272007799 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 187272007800 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 187272007801 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 187272007802 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 187272007803 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 187272007804 molybdopterin cofactor binding site; other site 187272007805 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cd02775 187272007806 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 187272007807 4Fe-4S binding domain; Region: Fer4; pfam00037 187272007808 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 187272007809 Response regulator receiver domain; Region: Response_reg; pfam00072 187272007810 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272007811 active site 187272007812 phosphorylation site [posttranslational modification] 187272007813 intermolecular recognition site; other site 187272007814 dimerization interface [polypeptide binding]; other site 187272007815 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 187272007816 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 187272007817 Zn2+ binding site [ion binding]; other site 187272007818 Mg2+ binding site [ion binding]; other site 187272007819 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 187272007820 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 187272007821 dimer interface [polypeptide binding]; other site 187272007822 phosphorylation site [posttranslational modification] 187272007823 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 187272007824 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272007825 ATP binding site [chemical binding]; other site 187272007826 Mg2+ binding site [ion binding]; other site 187272007827 G-X-G motif; other site 187272007828 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 187272007829 MAPEG family; Region: MAPEG; cl09190 187272007830 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 187272007831 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 187272007832 S-adenosylmethionine binding site [chemical binding]; other site 187272007833 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 187272007834 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 187272007835 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 187272007836 substrate-cofactor binding pocket; other site 187272007837 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272007838 catalytic residue [active] 187272007839 biotin synthase; Region: bioB; TIGR00433 187272007840 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 187272007841 FeS/SAM binding site; other site 187272007842 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 187272007843 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 187272007844 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 187272007845 active site 187272007846 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 187272007847 UbiA prenyltransferase family; Region: UbiA; pfam01040 187272007848 Chorismate lyase; Region: Chor_lyase; cl01230 187272007849 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 187272007850 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 187272007851 generic binding surface II; other site 187272007852 ssDNA binding site; other site 187272007853 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 187272007854 ATP binding site [chemical binding]; other site 187272007855 putative Mg++ binding site [ion binding]; other site 187272007856 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 187272007857 nucleotide binding region [chemical binding]; other site 187272007858 ATP-binding site [chemical binding]; other site 187272007859 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 187272007860 homotrimer interaction site [polypeptide binding]; other site 187272007861 putative active site [active] 187272007862 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 187272007863 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 187272007864 Zn2+ binding site [ion binding]; other site 187272007865 Mg2+ binding site [ion binding]; other site 187272007866 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 187272007867 synthetase active site [active] 187272007868 NTP binding site [chemical binding]; other site 187272007869 metal binding site [ion binding]; metal-binding site 187272007870 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 187272007871 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 187272007872 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 187272007873 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 187272007874 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 187272007875 catalytic site [active] 187272007876 G-X2-G-X-G-K; other site 187272007877 hypothetical protein; Provisional; Region: PRK11820 187272007878 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 187272007879 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 187272007880 ribonuclease PH; Reviewed; Region: rph; PRK00173 187272007881 Ribonuclease PH; Region: RNase_PH_bact; cd11362 187272007882 hexamer interface [polypeptide binding]; other site 187272007883 active site 187272007884 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 187272007885 active site 187272007886 dimerization interface [polypeptide binding]; other site 187272007887 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 187272007888 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 187272007889 FeS/SAM binding site; other site 187272007890 HemN C-terminal domain; Region: HemN_C; pfam06969 187272007891 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 187272007892 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 187272007893 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 187272007894 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 187272007895 substrate binding pocket [chemical binding]; other site 187272007896 membrane-bound complex binding site; other site 187272007897 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272007898 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272007899 metal binding site [ion binding]; metal-binding site 187272007900 active site 187272007901 I-site; other site 187272007902 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 187272007903 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 187272007904 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase; Region: DapE-ArgE; TIGR01910 187272007905 putative metal binding site [ion binding]; other site 187272007906 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 187272007907 Amidase; Region: Amidase; cl11426 187272007908 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 187272007909 Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating...; Region: Rieske_RO_Alpha_OMO_CARDO; cd03548 187272007910 iron-sulfur cluster [ion binding]; other site 187272007911 alpha subunit interaction site [polypeptide binding]; other site 187272007912 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 187272007913 alpha subunit interface [polypeptide binding]; other site 187272007914 active site 187272007915 substrate binding site [chemical binding]; other site 187272007916 Fe binding site [ion binding]; other site 187272007917 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 187272007918 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 187272007919 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 187272007920 IscR-regulated protein YhgI; Region: YhgI_GntY; TIGR03341 187272007921 NifU-like domain; Region: NifU; cl00484 187272007922 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 187272007923 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 187272007924 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 187272007925 active site 187272007926 Fe binding site [ion binding]; other site 187272007927 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 187272007928 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 187272007929 catalytic loop [active] 187272007930 iron binding site [ion binding]; other site 187272007931 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 187272007932 FAD binding pocket [chemical binding]; other site 187272007933 FAD binding motif [chemical binding]; other site 187272007934 phosphate binding motif [ion binding]; other site 187272007935 beta-alpha-beta structure motif; other site 187272007936 NAD binding pocket [chemical binding]; other site 187272007937 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 187272007938 acetaldehyde dehydrogenase; Validated; Region: PRK08300 187272007939 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 187272007940 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 187272007941 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 187272007942 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 187272007943 active site 187272007944 catalytic residues [active] 187272007945 metal binding site [ion binding]; metal-binding site 187272007946 DmpG-like communication domain; Region: DmpG_comm; pfam07836 187272007947 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 187272007948 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 187272007949 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 187272007950 catalytic triad [active] 187272007951 dimer interface [polypeptide binding]; other site 187272007952 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 187272007953 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 187272007954 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 187272007955 Protein export membrane protein; Region: SecD_SecF; cl14618 187272007956 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 187272007957 MarR family; Region: MarR_2; cl17246 187272007958 MarR family; Region: MarR_2; cl17246 187272007959 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 187272007960 Malonate decarboxylase gamma subunit (MdcE); Region: MdcE; cl17835 187272007961 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 187272007962 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 187272007963 NADP binding site [chemical binding]; other site 187272007964 dimer interface [polypeptide binding]; other site 187272007965 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 187272007966 active site 187272007967 tetramer interface; other site 187272007968 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 187272007969 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 187272007970 dimerization interface [polypeptide binding]; other site 187272007971 ATP binding site [chemical binding]; other site 187272007972 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 187272007973 dimerization interface [polypeptide binding]; other site 187272007974 ATP binding site [chemical binding]; other site 187272007975 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 187272007976 putative active site [active] 187272007977 catalytic triad [active] 187272007978 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 187272007979 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 187272007980 dihydrodipicolinate synthase; Region: dapA; TIGR00674 187272007981 dimer interface [polypeptide binding]; other site 187272007982 active site 187272007983 catalytic residue [active] 187272007984 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 187272007985 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 187272007986 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 187272007987 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 187272007988 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 187272007989 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 187272007990 catalytic triad [active] 187272007991 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 187272007992 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 187272007993 putative active site [active] 187272007994 PhoH-like protein; Region: PhoH; cl17668 187272007995 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 187272007996 Domain of unknown function DUF20; Region: UPF0118; pfam01594 187272007997 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 187272007998 Peptidase family M48; Region: Peptidase_M48; pfam01435 187272007999 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 187272008000 TPR motif; other site 187272008001 binding surface 187272008002 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 187272008003 binding surface 187272008004 TPR motif; other site 187272008005 Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E); Region: PHA_synth_III_E; pfam09712 187272008006 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 187272008007 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 187272008008 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 187272008009 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 187272008010 NAD(P) binding site [chemical binding]; other site 187272008011 homotetramer interface [polypeptide binding]; other site 187272008012 homodimer interface [polypeptide binding]; other site 187272008013 active site 187272008014 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 187272008015 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 187272008016 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 187272008017 HDOD domain; Region: HDOD; pfam08668 187272008018 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 187272008019 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 187272008020 chorismate binding enzyme; Region: Chorismate_bind; cl10555 187272008021 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 187272008022 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 187272008023 acyl-activating enzyme (AAE) consensus motif; other site 187272008024 putative AMP binding site [chemical binding]; other site 187272008025 putative active site [active] 187272008026 putative CoA binding site [chemical binding]; other site 187272008027 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 187272008028 hypothetical protein; Validated; Region: PRK00110 187272008029 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 187272008030 active site 187272008031 putative DNA-binding cleft [nucleotide binding]; other site 187272008032 dimer interface [polypeptide binding]; other site 187272008033 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 187272008034 RuvA N terminal domain; Region: RuvA_N; pfam01330 187272008035 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 187272008036 primosome assembly protein PriA; Validated; Region: PRK05580 187272008037 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 187272008038 ATP binding site [chemical binding]; other site 187272008039 putative Mg++ binding site [ion binding]; other site 187272008040 helicase superfamily c-terminal domain; Region: HELICc; smart00490 187272008041 DNA-J related protein; Region: DNAJ_related; pfam12339 187272008042 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 187272008043 HSP70 interaction site [polypeptide binding]; other site 187272008044 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 187272008045 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 187272008046 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 187272008047 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 187272008048 CPxP motif; other site 187272008049 Porin subfamily; Region: Porin_2; pfam02530 187272008050 Protein of unknown function (DUF3179); Region: DUF3179; pfam11376 187272008051 sensor protein PhoQ; Provisional; Region: PRK10815 187272008052 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272008053 ATP binding site [chemical binding]; other site 187272008054 Mg2+ binding site [ion binding]; other site 187272008055 G-X-G motif; other site 187272008056 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 187272008057 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272008058 active site 187272008059 phosphorylation site [posttranslational modification] 187272008060 intermolecular recognition site; other site 187272008061 dimerization interface [polypeptide binding]; other site 187272008062 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 187272008063 DNA binding site [nucleotide binding] 187272008064 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 187272008065 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 187272008066 putative hydrolase; Provisional; Region: PRK10985 187272008067 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 187272008068 PAS domain; Region: PAS_9; pfam13426 187272008069 putative active site [active] 187272008070 heme pocket [chemical binding]; other site 187272008071 PAS domain; Region: PAS_9; pfam13426 187272008072 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 187272008073 putative active site [active] 187272008074 heme pocket [chemical binding]; other site 187272008075 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272008076 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272008077 metal binding site [ion binding]; metal-binding site 187272008078 active site 187272008079 I-site; other site 187272008080 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 187272008081 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 187272008082 putative dimer interface [polypeptide binding]; other site 187272008083 [2Fe-2S] cluster binding site [ion binding]; other site 187272008084 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 187272008085 SLBB domain; Region: SLBB; pfam10531 187272008086 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 187272008087 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 187272008088 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 187272008089 catalytic loop [active] 187272008090 iron binding site [ion binding]; other site 187272008091 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 187272008092 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 187272008093 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 187272008094 [4Fe-4S] binding site [ion binding]; other site 187272008095 molybdopterin cofactor binding site; other site 187272008096 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 187272008097 molybdopterin cofactor binding site; other site 187272008098 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 187272008099 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 187272008100 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 187272008101 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 187272008102 Zn binding site [ion binding]; other site 187272008103 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 187272008104 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 187272008105 Zn binding site [ion binding]; other site 187272008106 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 187272008107 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 187272008108 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 187272008109 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 187272008110 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 187272008111 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 187272008112 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 187272008113 DNA binding residues [nucleotide binding] 187272008114 DNA primase; Validated; Region: dnaG; PRK05667 187272008115 CHC2 zinc finger; Region: zf-CHC2; pfam01807 187272008116 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 187272008117 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 187272008118 active site 187272008119 metal binding site [ion binding]; metal-binding site 187272008120 interdomain interaction site; other site 187272008121 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 187272008122 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 187272008123 Yqey-like protein; Region: YqeY; pfam09424 187272008124 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 187272008125 UGMP family protein; Validated; Region: PRK09604 187272008126 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 187272008127 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 187272008128 Dihydroneopterin aldolase; Region: FolB; smart00905 187272008129 active site 187272008130 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 187272008131 catalytic center binding site [active] 187272008132 ATP binding site [chemical binding]; other site 187272008133 Uncharacterized conserved protein [Function unknown]; Region: COG1565 187272008134 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 187272008135 Active_site [active] 187272008136 Ion transport protein; Region: Ion_trans; pfam00520 187272008137 Ion channel; Region: Ion_trans_2; pfam07885 187272008138 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 187272008139 TrkA-N domain; Region: TrkA_N; pfam02254 187272008140 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 187272008141 TrkA-N domain; Region: TrkA_N; pfam02254 187272008142 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 187272008143 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272008144 ligand binding site [chemical binding]; other site 187272008145 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 187272008146 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 187272008147 catalytic loop [active] 187272008148 iron binding site [ion binding]; other site 187272008149 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 187272008150 FAD binding pocket [chemical binding]; other site 187272008151 FAD binding motif [chemical binding]; other site 187272008152 phosphate binding motif [ion binding]; other site 187272008153 beta-alpha-beta structure motif; other site 187272008154 NAD binding pocket [chemical binding]; other site 187272008155 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 187272008156 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 187272008157 oligopeptidase A; Provisional; Region: PRK10911 187272008158 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 187272008159 active site 187272008160 Zn binding site [ion binding]; other site 187272008161 glutathione reductase; Validated; Region: PRK06116 187272008162 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 187272008163 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272008164 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272008165 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272008166 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 187272008167 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 187272008168 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 187272008169 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 187272008170 DNA-binding site [nucleotide binding]; DNA binding site 187272008171 RNA-binding motif; other site 187272008172 Uncharacterized conserved protein [Function unknown]; Region: COG2947 187272008173 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 187272008174 Cell division protein ZapA; Region: ZapA; pfam05164 187272008175 TIGR02449 family protein; Region: TIGR02449 187272008176 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 187272008177 proline aminopeptidase P II; Provisional; Region: PRK10879 187272008178 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 187272008179 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 187272008180 active site 187272008181 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 187272008182 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 187272008183 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 187272008184 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 187272008185 sensory histidine kinase AtoS; Provisional; Region: PRK11360 187272008186 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 187272008187 dimer interface [polypeptide binding]; other site 187272008188 phosphorylation site [posttranslational modification] 187272008189 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272008190 ATP binding site [chemical binding]; other site 187272008191 Mg2+ binding site [ion binding]; other site 187272008192 G-X-G motif; other site 187272008193 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 187272008194 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 187272008195 CoA-ligase; Region: Ligase_CoA; pfam00549 187272008196 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 187272008197 CoA binding domain; Region: CoA_binding; smart00881 187272008198 CoA-ligase; Region: Ligase_CoA; pfam00549 187272008199 NAD synthetase; Provisional; Region: PRK13981 187272008200 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 187272008201 multimer interface [polypeptide binding]; other site 187272008202 active site 187272008203 catalytic triad [active] 187272008204 protein interface 1 [polypeptide binding]; other site 187272008205 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 187272008206 homodimer interface [polypeptide binding]; other site 187272008207 NAD binding pocket [chemical binding]; other site 187272008208 ATP binding pocket [chemical binding]; other site 187272008209 Mg binding site [ion binding]; other site 187272008210 active-site loop [active] 187272008211 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 187272008212 Nitrogen regulatory protein P-II; Region: P-II; smart00938 187272008213 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 187272008214 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 187272008215 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 187272008216 RNA binding surface [nucleotide binding]; other site 187272008217 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 187272008218 active site 187272008219 Adenylation domain of RNA circularization proteins; Region: Adenylation_RNA_ligase; cd07894 187272008220 active site 187272008221 dimer interface [polypeptide binding]; other site 187272008222 aspartate aminotransferase; Provisional; Region: PRK05764 187272008223 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 187272008224 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272008225 homodimer interface [polypeptide binding]; other site 187272008226 catalytic residue [active] 187272008227 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 187272008228 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 187272008229 motif II; other site 187272008230 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 187272008231 hypothetical protein; Provisional; Region: PRK04358 187272008232 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 187272008233 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 187272008234 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 187272008235 Clp amino terminal domain; Region: Clp_N; pfam02861 187272008236 Clp amino terminal domain; Region: Clp_N; pfam02861 187272008237 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 187272008238 Walker A motif; other site 187272008239 ATP binding site [chemical binding]; other site 187272008240 Walker B motif; other site 187272008241 arginine finger; other site 187272008242 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 187272008243 Walker A motif; other site 187272008244 ATP binding site [chemical binding]; other site 187272008245 Walker B motif; other site 187272008246 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 187272008247 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 187272008248 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 187272008249 non-specific DNA binding site [nucleotide binding]; other site 187272008250 salt bridge; other site 187272008251 sequence-specific DNA binding site [nucleotide binding]; other site 187272008252 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 187272008253 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 187272008254 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 187272008255 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 187272008256 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 187272008257 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 187272008258 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 187272008259 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 187272008260 conserved cys residue [active] 187272008261 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 187272008262 NodB motif; other site 187272008263 putative active site [active] 187272008264 putative catalytic site [active] 187272008265 Zn binding site [ion binding]; other site 187272008266 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 187272008267 C-terminal peptidase (prc); Region: prc; TIGR00225 187272008268 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 187272008269 protein binding site [polypeptide binding]; other site 187272008270 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 187272008271 Catalytic dyad [active] 187272008272 Peptidase family M23; Region: Peptidase_M23; pfam01551 187272008273 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272008274 active site residue [active] 187272008275 preprotein translocase subunit SecB; Validated; Region: PRK05751 187272008276 SecA binding site; other site 187272008277 Preprotein binding site; other site 187272008278 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 187272008279 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 187272008280 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 187272008281 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 187272008282 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 187272008283 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 187272008284 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 187272008285 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 187272008286 dimer interface [polypeptide binding]; other site 187272008287 conserved gate region; other site 187272008288 putative PBP binding loops; other site 187272008289 ABC-ATPase subunit interface; other site 187272008290 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 187272008291 dimer interface [polypeptide binding]; other site 187272008292 conserved gate region; other site 187272008293 putative PBP binding loops; other site 187272008294 ABC-ATPase subunit interface; other site 187272008295 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 187272008296 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 187272008297 glycine cleavage system protein H; Provisional; Region: PRK13380 187272008298 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 187272008299 lipoyl attachment site [posttranslational modification]; other site 187272008300 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 187272008301 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 187272008302 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272008303 tetramer interface [polypeptide binding]; other site 187272008304 catalytic residue [active] 187272008305 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 187272008306 dimer interface [polypeptide binding]; other site 187272008307 catalytic triad [active] 187272008308 peroxidatic and resolving cysteines [active] 187272008309 glycine dehydrogenase subunit 2; Validated; Region: PRK04366 187272008310 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 187272008311 catalytic residue [active] 187272008312 rarD protein; Region: rarD; TIGR00688 187272008313 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 187272008314 Sel1-like repeats; Region: SEL1; smart00671 187272008315 Sel1-like repeats; Region: SEL1; smart00671 187272008316 Sel1-like repeats; Region: SEL1; smart00671 187272008317 Sel1-like repeats; Region: SEL1; smart00671 187272008318 Sel1-like repeats; Region: SEL1; smart00671 187272008319 Uncharacterized conserved protein [Function unknown]; Region: COG5316 187272008320 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 187272008321 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 187272008322 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 187272008323 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 187272008324 FAD binding pocket [chemical binding]; other site 187272008325 FAD binding motif [chemical binding]; other site 187272008326 phosphate binding motif [ion binding]; other site 187272008327 beta-alpha-beta structure motif; other site 187272008328 NAD binding pocket [chemical binding]; other site 187272008329 Iron coordination center [ion binding]; other site 187272008330 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 187272008331 cyanate hydratase; Validated; Region: PRK02866 187272008332 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 187272008333 oligomer interface [polypeptide binding]; other site 187272008334 active site 187272008335 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 187272008336 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 187272008337 Walker A/P-loop; other site 187272008338 ATP binding site [chemical binding]; other site 187272008339 Q-loop/lid; other site 187272008340 ABC transporter signature motif; other site 187272008341 Walker B; other site 187272008342 D-loop; other site 187272008343 H-loop/switch region; other site 187272008344 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 187272008345 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 187272008346 dimer interface [polypeptide binding]; other site 187272008347 conserved gate region; other site 187272008348 putative PBP binding loops; other site 187272008349 ABC-ATPase subunit interface; other site 187272008350 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 187272008351 NMT1-like family; Region: NMT1_2; pfam13379 187272008352 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 187272008353 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 187272008354 ANTAR domain; Region: ANTAR; pfam03861 187272008355 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 187272008356 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 187272008357 active site 187272008358 substrate-binding site [chemical binding]; other site 187272008359 metal-binding site [ion binding] 187272008360 ATP binding site [chemical binding]; other site 187272008361 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 187272008362 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 187272008363 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 187272008364 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 187272008365 E3 interaction surface; other site 187272008366 lipoyl attachment site [posttranslational modification]; other site 187272008367 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11857 187272008368 e3 binding domain; Region: E3_binding; pfam02817 187272008369 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 187272008370 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 187272008371 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 187272008372 tetramer interface [polypeptide binding]; other site 187272008373 TPP-binding site [chemical binding]; other site 187272008374 heterodimer interface [polypeptide binding]; other site 187272008375 phosphorylation loop region [posttranslational modification] 187272008376 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 187272008377 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 187272008378 alpha subunit interface [polypeptide binding]; other site 187272008379 TPP binding site [chemical binding]; other site 187272008380 heterodimer interface [polypeptide binding]; other site 187272008381 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 187272008382 acetyl-CoA synthetase; Provisional; Region: PRK04319 187272008383 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 187272008384 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272008385 acyl-activating enzyme (AAE) consensus motif; other site 187272008386 AMP binding site [chemical binding]; other site 187272008387 active site 187272008388 CoA binding site [chemical binding]; other site 187272008389 CAAX protease self-immunity; Region: Abi; pfam02517 187272008390 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 187272008391 putative FMN binding site [chemical binding]; other site 187272008392 NADPH bind site [chemical binding]; other site 187272008393 Phasin protein; Region: Phasin_2; cl11491 187272008394 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 187272008395 2-methylcitrate dehydratase; Region: prpD; TIGR02330 187272008396 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 187272008397 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 187272008398 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 187272008399 substrate binding site [chemical binding]; other site 187272008400 ligand binding site [chemical binding]; other site 187272008401 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 187272008402 substrate binding site [chemical binding]; other site 187272008403 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 187272008404 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 187272008405 dimer interface [polypeptide binding]; other site 187272008406 active site 187272008407 citrylCoA binding site [chemical binding]; other site 187272008408 oxalacetate/citrate binding site [chemical binding]; other site 187272008409 coenzyme A binding site [chemical binding]; other site 187272008410 catalytic triad [active] 187272008411 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 187272008412 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 187272008413 tetramer interface [polypeptide binding]; other site 187272008414 active site 187272008415 Mg2+/Mn2+ binding site [ion binding]; other site 187272008416 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 187272008417 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 187272008418 NADP binding site [chemical binding]; other site 187272008419 dimer interface [polypeptide binding]; other site 187272008420 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 187272008421 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 187272008422 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 187272008423 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 187272008424 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 187272008425 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 187272008426 E3 interaction surface; other site 187272008427 lipoyl attachment site [posttranslational modification]; other site 187272008428 e3 binding domain; Region: E3_binding; pfam02817 187272008429 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 187272008430 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 187272008431 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 187272008432 TPP-binding site [chemical binding]; other site 187272008433 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 187272008434 dimer interface [polypeptide binding]; other site 187272008435 PYR/PP interface [polypeptide binding]; other site 187272008436 TPP binding site [chemical binding]; other site 187272008437 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 187272008438 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 187272008439 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 187272008440 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 187272008441 metal binding site [ion binding]; metal-binding site 187272008442 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 187272008443 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 187272008444 substrate binding site [chemical binding]; other site 187272008445 glutamase interaction surface [polypeptide binding]; other site 187272008446 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 187272008447 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 187272008448 catalytic residues [active] 187272008449 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 187272008450 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 187272008451 putative active site [active] 187272008452 oxyanion strand; other site 187272008453 catalytic triad [active] 187272008454 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 187272008455 putative active site pocket [active] 187272008456 4-fold oligomerization interface [polypeptide binding]; other site 187272008457 metal binding residues [ion binding]; metal-binding site 187272008458 3-fold/trimer interface [polypeptide binding]; other site 187272008459 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 187272008460 putative active site [active] 187272008461 dimerization interface [polypeptide binding]; other site 187272008462 putative tRNAtyr binding site [nucleotide binding]; other site 187272008463 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 187272008464 putative acyl-acceptor binding pocket; other site 187272008465 TPR repeat; Region: TPR_11; pfam13414 187272008466 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 187272008467 binding surface 187272008468 TPR motif; other site 187272008469 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 187272008470 TrkA-N domain; Region: TrkA_N; pfam02254 187272008471 TrkA-C domain; Region: TrkA_C; pfam02080 187272008472 TrkA-N domain; Region: TrkA_N; pfam02254 187272008473 TrkA-C domain; Region: TrkA_C; pfam02080 187272008474 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 187272008475 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272008476 active site 187272008477 phosphorylation site [posttranslational modification] 187272008478 intermolecular recognition site; other site 187272008479 dimerization interface [polypeptide binding]; other site 187272008480 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 187272008481 Walker A motif; other site 187272008482 ATP binding site [chemical binding]; other site 187272008483 Walker B motif; other site 187272008484 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272008485 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 187272008486 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 187272008487 dimerization interface [polypeptide binding]; other site 187272008488 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 187272008489 dimer interface [polypeptide binding]; other site 187272008490 phosphorylation site [posttranslational modification] 187272008491 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 187272008492 ATP binding site [chemical binding]; other site 187272008493 Mg2+ binding site [ion binding]; other site 187272008494 G-X-G motif; other site 187272008495 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 187272008496 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 187272008497 putative RNA binding site [nucleotide binding]; other site 187272008498 16S rRNA methyltransferase B; Provisional; Region: PRK10901 187272008499 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 187272008500 S-adenosylmethionine binding site [chemical binding]; other site 187272008501 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 187272008502 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 187272008503 putative active site [active] 187272008504 substrate binding site [chemical binding]; other site 187272008505 putative cosubstrate binding site; other site 187272008506 catalytic site [active] 187272008507 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 187272008508 substrate binding site [chemical binding]; other site 187272008509 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 187272008510 active site 187272008511 catalytic residues [active] 187272008512 metal binding site [ion binding]; metal-binding site 187272008513 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 187272008514 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 187272008515 DNA protecting protein DprA; Region: dprA; TIGR00732 187272008516 Protein of unknown function (DUF494); Region: DUF494; pfam04361 187272008517 DNA topoisomerase I; Provisional; Region: PRK08780 187272008518 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 187272008519 active site 187272008520 interdomain interaction site; other site 187272008521 putative metal-binding site [ion binding]; other site 187272008522 nucleotide binding site [chemical binding]; other site 187272008523 Bacterial DNA topoisomeraes I ATP-binding domain; Region: TOP1Bc; smart00436 187272008524 domain I; other site 187272008525 phosphate binding site [ion binding]; other site 187272008526 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 187272008527 domain II; other site 187272008528 domain III; other site 187272008529 nucleotide binding site [chemical binding]; other site 187272008530 DNA binding groove [nucleotide binding] 187272008531 catalytic site [active] 187272008532 domain IV; other site 187272008533 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 187272008534 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 187272008535 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 187272008536 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 187272008537 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 187272008538 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 187272008539 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 187272008540 heme-binding site [chemical binding]; other site 187272008541 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 187272008542 AMP binding site [chemical binding]; other site 187272008543 metal binding site [ion binding]; metal-binding site 187272008544 active site 187272008545 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 187272008546 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 187272008547 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 187272008548 putative acyl-acceptor binding pocket; other site 187272008549 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 187272008550 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 187272008551 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 187272008552 S-adenosylmethionine binding site [chemical binding]; other site 187272008553 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 187272008554 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 187272008555 Protein of unknown function, DUF; Region: DUF411; cl01142 187272008556 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 187272008557 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 187272008558 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 187272008559 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 187272008560 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 187272008561 Walker A/P-loop; other site 187272008562 ATP binding site [chemical binding]; other site 187272008563 Q-loop/lid; other site 187272008564 ABC transporter signature motif; other site 187272008565 Walker B; other site 187272008566 D-loop; other site 187272008567 H-loop/switch region; other site 187272008568 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 187272008569 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 187272008570 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 187272008571 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 187272008572 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 187272008573 DNA binding site [nucleotide binding] 187272008574 catalytic residue [active] 187272008575 H2TH interface [polypeptide binding]; other site 187272008576 putative catalytic residues [active] 187272008577 turnover-facilitating residue; other site 187272008578 intercalation triad [nucleotide binding]; other site 187272008579 8OG recognition residue [nucleotide binding]; other site 187272008580 putative reading head residues; other site 187272008581 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 187272008582 acetyl-CoA synthetase; Provisional; Region: PRK04319 187272008583 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 187272008584 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 187272008585 acyl-activating enzyme (AAE) consensus motif; other site 187272008586 AMP binding site [chemical binding]; other site 187272008587 active site 187272008588 CoA binding site [chemical binding]; other site 187272008589 Predicted permease; Region: DUF318; cl17795 187272008590 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272008591 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272008592 metal binding site [ion binding]; metal-binding site 187272008593 active site 187272008594 I-site; other site 187272008595 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272008596 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272008597 metal binding site [ion binding]; metal-binding site 187272008598 active site 187272008599 I-site; other site 187272008600 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 187272008601 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 187272008602 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 187272008603 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 187272008604 active site 187272008605 (T/H)XGH motif; other site 187272008606 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 187272008607 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 187272008608 S-adenosylmethionine binding site [chemical binding]; other site 187272008609 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 187272008610 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 187272008611 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 187272008612 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 187272008613 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 187272008614 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 187272008615 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 187272008616 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 187272008617 P loop; other site 187272008618 GTP binding site [chemical binding]; other site 187272008619 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 187272008620 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272008621 Walker A/P-loop; other site 187272008622 ATP binding site [chemical binding]; other site 187272008623 Q-loop/lid; other site 187272008624 ABC transporter signature motif; other site 187272008625 Walker B; other site 187272008626 D-loop; other site 187272008627 H-loop/switch region; other site 187272008628 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 187272008629 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 187272008630 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 187272008631 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 187272008632 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 187272008633 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 187272008634 DNA binding residues [nucleotide binding] 187272008635 hypothetical protein; Reviewed; Region: PRK00024 187272008636 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 187272008637 MPN+ (JAMM) motif; other site 187272008638 Zinc-binding site [ion binding]; other site 187272008639 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 187272008640 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 187272008641 dimer interface [polypeptide binding]; other site 187272008642 anticodon binding site; other site 187272008643 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 187272008644 homodimer interface [polypeptide binding]; other site 187272008645 motif 1; other site 187272008646 active site 187272008647 motif 2; other site 187272008648 GAD domain; Region: GAD; pfam02938 187272008649 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 187272008650 active site 187272008651 motif 3; other site 187272008652 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 187272008653 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 187272008654 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 187272008655 HemY protein N-terminus; Region: HemY_N; pfam07219 187272008656 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 187272008657 binding surface 187272008658 TPR motif; other site 187272008659 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 187272008660 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 187272008661 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 187272008662 active site 187272008663 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 187272008664 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 187272008665 domain interfaces; other site 187272008666 active site 187272008667 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 187272008668 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272008669 active site 187272008670 phosphorylation site [posttranslational modification] 187272008671 intermolecular recognition site; other site 187272008672 dimerization interface [polypeptide binding]; other site 187272008673 LytTr DNA-binding domain; Region: LytTR; smart00850 187272008674 Histidine kinase; Region: His_kinase; pfam06580 187272008675 argininosuccinate lyase; Provisional; Region: PRK00855 187272008676 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 187272008677 active sites [active] 187272008678 tetramer interface [polypeptide binding]; other site 187272008679 FOG: CBS domain [General function prediction only]; Region: COG0517 187272008680 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce...; Region: CBS_pair_ACT_assoc; cd04584 187272008681 FOG: CBS domain [General function prediction only]; Region: COG0517 187272008682 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 187272008683 FOG: CBS domain [General function prediction only]; Region: COG0517 187272008684 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 187272008685 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 187272008686 PAS domain; Region: PAS_9; pfam13426 187272008687 putative active site [active] 187272008688 heme pocket [chemical binding]; other site 187272008689 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272008690 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272008691 metal binding site [ion binding]; metal-binding site 187272008692 active site 187272008693 I-site; other site 187272008694 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 187272008695 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 187272008696 DNA-binding site [nucleotide binding]; DNA binding site 187272008697 RNA-binding motif; other site 187272008698 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 187272008699 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 187272008700 putative NAD(P) binding site [chemical binding]; other site 187272008701 active site 187272008702 putative substrate binding site [chemical binding]; other site 187272008703 muropeptide transporter; Reviewed; Region: ampG; PRK11902 187272008704 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 187272008705 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 187272008706 putative substrate translocation pore; other site 187272008707 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 187272008708 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 187272008709 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 187272008710 metal binding site [ion binding]; metal-binding site 187272008711 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 187272008712 tetramer interface [polypeptide binding]; other site 187272008713 active site 187272008714 Mg2+/Mn2+ binding site [ion binding]; other site 187272008715 isocitrate lyase; Region: PLN02892 187272008716 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 187272008717 PAS domain; Region: PAS_9; pfam13426 187272008718 putative active site [active] 187272008719 heme pocket [chemical binding]; other site 187272008720 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 187272008721 PAS domain; Region: PAS_9; pfam13426 187272008722 putative active site [active] 187272008723 heme pocket [chemical binding]; other site 187272008724 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 187272008725 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 187272008726 metal binding site [ion binding]; metal-binding site 187272008727 active site 187272008728 I-site; other site 187272008729 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 187272008730 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 187272008731 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 187272008732 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 187272008733 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 187272008734 DNA binding residues [nucleotide binding] 187272008735 dimerization interface [polypeptide binding]; other site 187272008736 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008737 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008738 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008739 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008740 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008741 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008742 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008743 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008744 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008745 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008746 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008747 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008748 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008749 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008750 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008751 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008752 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008753 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008754 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008755 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008756 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008757 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008758 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008759 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008760 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008761 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008762 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008763 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008764 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008765 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 187272008766 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 187272008767 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 187272008768 MPT binding site; other site 187272008769 trimer interface [polypeptide binding]; other site 187272008770 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 187272008771 active site lid residues [active] 187272008772 substrate binding pocket [chemical binding]; other site 187272008773 catalytic residues [active] 187272008774 substrate-Mg2+ binding site; other site 187272008775 aspartate-rich region 1; other site 187272008776 aspartate-rich region 2; other site 187272008777 Fructosamine kinase; Region: Fructosamin_kin; cl17579 187272008778 Phosphotransferase enzyme family; Region: APH; pfam01636 187272008779 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 187272008780 S-adenosylmethionine binding site [chemical binding]; other site 187272008781 Protein required for attachment to host cells; Region: Host_attach; pfam10116 187272008782 AsmA family; Region: AsmA; pfam05170 187272008783 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 187272008784 A/G-specific adenine glycosylase; Region: mutY; TIGR01084 187272008785 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 187272008786 minor groove reading motif; other site 187272008787 helix-hairpin-helix signature motif; other site 187272008788 substrate binding pocket [chemical binding]; other site 187272008789 active site 187272008790 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 187272008791 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 187272008792 DNA binding and oxoG recognition site [nucleotide binding] 187272008793 oxidative damage protection protein; Provisional; Region: PRK05408 187272008794 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 187272008795 Ligand Binding Site [chemical binding]; other site 187272008796 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 187272008797 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272008798 metal binding triad; other site 187272008799 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 187272008800 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 187272008801 metal binding triad; other site 187272008802 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 187272008803 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 187272008804 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 187272008805 homodimer interface [polypeptide binding]; other site 187272008806 substrate-cofactor binding pocket; other site 187272008807 catalytic residue [active] 187272008808 Na/Pi-cotransporter; Region: NaPi_cotrn_rel; TIGR00704 187272008809 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 187272008810 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 187272008811 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 187272008812 Proline dehydrogenase; Region: Pro_dh; pfam01619 187272008813 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 187272008814 Glutamate binding site [chemical binding]; other site 187272008815 NAD binding site [chemical binding]; other site 187272008816 catalytic residues [active] 187272008817 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 187272008818 catalytic residues [active] 187272008819 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 187272008820 putative acyltransferase; Provisional; Region: PRK05790 187272008821 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 187272008822 dimer interface [polypeptide binding]; other site 187272008823 active site 187272008824 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 187272008825 Ligand Binding Site [chemical binding]; other site 187272008826 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 187272008827 Ligand Binding Site [chemical binding]; other site 187272008828 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 187272008829 arsenical-resistance protein; Region: acr3; TIGR00832 187272008830 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 187272008831 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 187272008832 P loop; other site 187272008833 Nucleotide binding site [chemical binding]; other site 187272008834 DTAP/Switch II; other site 187272008835 Switch I; other site 187272008836 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 187272008837 DTAP/Switch II; other site 187272008838 Switch I; other site 187272008839 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 187272008840 Low molecular weight phosphatase family; Region: LMWPc; cd00115 187272008841 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 187272008842 active site 187272008843 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 187272008844 dimerization interface [polypeptide binding]; other site 187272008845 putative DNA binding site [nucleotide binding]; other site 187272008846 putative Zn2+ binding site [ion binding]; other site 187272008847 Predicted flavoprotein [General function prediction only]; Region: COG0431 187272008848 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 187272008849 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272008850 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 187272008851 Walker A/P-loop; other site 187272008852 ATP binding site [chemical binding]; other site 187272008853 Q-loop/lid; other site 187272008854 ABC transporter signature motif; other site 187272008855 Walker B; other site 187272008856 D-loop; other site 187272008857 H-loop/switch region; other site 187272008858 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 187272008859 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 187272008860 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 187272008861 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 187272008862 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 187272008863 Sulfate transporter family; Region: Sulfate_transp; pfam00916 187272008864 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 187272008865 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 187272008866 Ligand Binding Site [chemical binding]; other site 187272008867 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 187272008868 Ligand Binding Site [chemical binding]; other site 187272008869 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 187272008870 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 187272008871 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 187272008872 trimer interface [polypeptide binding]; other site 187272008873 active site 187272008874 UDP-GlcNAc binding site [chemical binding]; other site 187272008875 lipid binding site [chemical binding]; lipid-binding site 187272008876 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 187272008877 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 187272008878 active site 187272008879 phosphorylation site [posttranslational modification] 187272008880 intermolecular recognition site; other site 187272008881 dimerization interface [polypeptide binding]; other site 187272008882 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 187272008883 DNA binding residues [nucleotide binding] 187272008884 dimerization interface [polypeptide binding]; other site 187272008885 HAMP domain; Region: HAMP; pfam00672 187272008886 dimerization interface [polypeptide binding]; other site 187272008887 Histidine kinase; Region: HisKA_3; pfam07730 187272008888 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 187272008889 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 187272008890 N-terminal plug; other site 187272008891 ligand-binding site [chemical binding]; other site 187272008892 Gram-negative porin; Region: Porin_4; pfam13609 187272008893 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 187272008894 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 187272008895 NAD(P) binding site [chemical binding]; other site 187272008896 catalytic residues [active] 187272008897 Protein of unknown function (DUF779); Region: DUF779; pfam05610 187272008898 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 187272008899 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 187272008900 N-terminal plug; other site 187272008901 ligand-binding site [chemical binding]; other site 187272008902 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 187272008903 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 187272008904 dimer interface [polypeptide binding]; other site 187272008905 Trp docking motif [polypeptide binding]; other site 187272008906 active site 187272008907 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 187272008908 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 187272008909 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 187272008910 substrate binding pocket [chemical binding]; other site 187272008911 membrane-bound complex binding site; other site 187272008912 hinge residues; other site 187272008913 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 187272008914 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 187272008915 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 187272008916 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 187272008917 active site residue [active] 187272008918 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 187272008919 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 187272008920 putative active site [active] 187272008921 heme pocket [chemical binding]; other site 187272008922 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 187272008923 Walker A motif; other site 187272008924 ATP binding site [chemical binding]; other site 187272008925 Walker B motif; other site 187272008926 arginine finger; other site 187272008927 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 187272008928 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 187272008929 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 187272008930 PBP superfamily domain; Region: PBP_like_2; pfam12849 187272008931 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 187272008932 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 187272008933 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 187272008934 Walker A/P-loop; other site 187272008935 ATP binding site [chemical binding]; other site 187272008936 Q-loop/lid; other site 187272008937 ABC transporter signature motif; other site 187272008938 Walker B; other site 187272008939 D-loop; other site 187272008940 H-loop/switch region; other site 187272008941 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 187272008942 dimer interface [polypeptide binding]; other site 187272008943 conserved gate region; other site 187272008944 putative PBP binding loops; other site 187272008945 ABC-ATPase subunit interface; other site 187272008946 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 187272008947 anti-sigma E factor; Provisional; Region: rseB; PRK09455 187272008948 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 187272008949 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 187272008950 Helix-turn-helix domain; Region: HTH_17; pfam12728 187272008951 PBP superfamily domain; Region: PBP_like; pfam12727 187272008952 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 187272008953 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 187272008954 dimer interface [polypeptide binding]; other site 187272008955 ssDNA binding site [nucleotide binding]; other site 187272008956 tetramer (dimer of dimers) interface [polypeptide binding]; other site 187272008957 Major Facilitator Superfamily; Region: MFS_1; pfam07690 187272008958 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 187272008959 putative substrate translocation pore; other site 187272008960 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 187272008961 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272008962 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 187272008963 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 187272008964 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 187272008965 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 187272008966 catalytic triad [active] 187272008967 Putative amidoligase enzyme; Region: Amidoligase_2; pfam12224 187272008968 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 187272008969 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 187272008970 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 187272008971 dimer interface [polypeptide binding]; other site 187272008972 active site 187272008973 citrylCoA binding site [chemical binding]; other site 187272008974 NADH binding [chemical binding]; other site 187272008975 cationic pore residues; other site 187272008976 oxalacetate/citrate binding site [chemical binding]; other site 187272008977 coenzyme A binding site [chemical binding]; other site 187272008978 catalytic triad [active] 187272008979 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 187272008980 Transglycosylase; Region: Transgly; pfam00912 187272008981 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 187272008982 Competence protein A; Region: Competence_A; pfam11104 187272008983 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 187272008984 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 187272008985 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 187272008986 Pilus assembly protein, PilO; Region: PilO; pfam04350 187272008987 Pilus assembly protein, PilP; Region: PilP; pfam04351 187272008988 AMIN domain; Region: AMIN; pfam11741 187272008989 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 187272008990 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 187272008991 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 187272008992 shikimate kinase; Reviewed; Region: aroK; PRK00131 187272008993 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 187272008994 ADP binding site [chemical binding]; other site 187272008995 magnesium binding site [ion binding]; other site 187272008996 putative shikimate binding site; other site 187272008997 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 187272008998 active site 187272008999 dimer interface [polypeptide binding]; other site 187272009000 metal binding site [ion binding]; metal-binding site 187272009001 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 187272009002 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 187272009003 active site 187272009004 dimer interface [polypeptide binding]; other site 187272009005 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 187272009006 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 187272009007 active site 187272009008 FMN binding site [chemical binding]; other site 187272009009 substrate binding site [chemical binding]; other site 187272009010 3Fe-4S cluster binding site [ion binding]; other site 187272009011 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 187272009012 domain interface; other site 187272009013 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 187272009014 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 187272009015 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 187272009016 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 187272009017 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 187272009018 substrate binding site [chemical binding]; other site 187272009019 active site 187272009020 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_human_like; cd03428 187272009021 active site 187272009022 Ap4A binding cleft/pocket [chemical binding]; other site 187272009023 P4 phosphate binding site; other site 187272009024 nudix motif; other site 187272009025 putative P2/P3 phosphate binding site [ion binding]; other site 187272009026 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 187272009027 putative metal binding site [ion binding]; other site 187272009028 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 187272009029 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 187272009030 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 187272009031 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 187272009032 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 187272009033 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 187272009034 ligand binding site [chemical binding]; other site 187272009035 homodimer interface [polypeptide binding]; other site 187272009036 NAD(P) binding site [chemical binding]; other site 187272009037 trimer interface B [polypeptide binding]; other site 187272009038 trimer interface A [polypeptide binding]; other site 187272009039 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 187272009040 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 187272009041 active site 187272009042 Sporulation related domain; Region: SPOR; pfam05036 187272009043 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 187272009044 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 187272009045 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 187272009046 active site 187272009047 HIGH motif; other site 187272009048 nucleotide binding site [chemical binding]; other site 187272009049 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 187272009050 KMSK motif region; other site 187272009051 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 187272009052 tRNA binding surface [nucleotide binding]; other site 187272009053 anticodon binding site; other site 187272009054 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 187272009055 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 187272009056 active site 187272009057 DNA binding site [nucleotide binding] 187272009058 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 187272009059 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 187272009060 Walker A motif; other site 187272009061 ATP binding site [chemical binding]; other site 187272009062 Walker B motif; other site 187272009063 arginine finger; other site 187272009064 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 187272009065 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 187272009066 intersubunit interface [polypeptide binding]; other site 187272009067 active site 187272009068 Zn2+ binding site [ion binding]; other site 187272009069 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 187272009070 Uncharacterized conserved protein [Function unknown]; Region: COG3379 187272009071 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 187272009072 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 187272009073 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 187272009074 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 187272009075 putative catalytic site [active] 187272009076 putative phosphate binding site [ion binding]; other site 187272009077 active site 187272009078 metal binding site A [ion binding]; metal-binding site 187272009079 DNA binding site [nucleotide binding] 187272009080 putative AP binding site [nucleotide binding]; other site 187272009081 putative metal binding site B [ion binding]; other site 187272009082 putative mechanosensitive channel protein; Provisional; Region: PRK11465 187272009083 Mechanosensitive ion channel; Region: MS_channel; pfam00924 187272009084 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 187272009085 DctM-like transporters; Region: DctM; pfam06808 187272009086 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 187272009087 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 187272009088 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 187272009089 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 187272009090 Transcriptional regulators [Transcription]; Region: GntR; COG1802 187272009091 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 187272009092 DNA-binding site [nucleotide binding]; DNA binding site 187272009093 FCD domain; Region: FCD; pfam07729 187272009094 malonyl-CoA synthase; Validated; Region: PRK07514 187272009095 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 187272009096 acyl-activating enzyme (AAE) consensus motif; other site 187272009097 active site 187272009098 AMP binding site [chemical binding]; other site 187272009099 CoA binding site [chemical binding]; other site 187272009100 Zinc-finger domain; Region: zf-CHCC; cl01821 187272009101 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 187272009102 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 187272009103 putative active site [active] 187272009104 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272009105 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 187272009106 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 187272009107 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 187272009108 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 187272009109 activation loop (A-loop); other site 187272009110 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 187272009111 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 187272009112 putative active site [active] 187272009113 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 187272009114 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 187272009115 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 187272009116 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 187272009117 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 187272009118 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 187272009119 active site 187272009120 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 187272009121 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 187272009122 NAD binding site [chemical binding]; other site 187272009123 putative substrate binding site 2 [chemical binding]; other site 187272009124 putative substrate binding site 1 [chemical binding]; other site 187272009125 active site 187272009126 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 187272009127 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 187272009128 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 187272009129 Walker A/P-loop; other site 187272009130 ATP binding site [chemical binding]; other site 187272009131 Q-loop/lid; other site 187272009132 ABC transporter signature motif; other site 187272009133 Walker B; other site 187272009134 D-loop; other site 187272009135 H-loop/switch region; other site 187272009136 Mn2+-dependent serine/threonine protein kinase [Signal transduction mechanisms]; Region: COG3642 187272009137 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 187272009138 putative acyl-acceptor binding pocket; other site 187272009139 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 187272009140 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 187272009141 putative active site [active] 187272009142 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 187272009143 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 187272009144 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase; Region: Kdo_hydroxy; pfam11004 187272009145 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 187272009146 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 187272009147 NADP binding site [chemical binding]; other site 187272009148 homopentamer interface [polypeptide binding]; other site 187272009149 substrate binding site [chemical binding]; other site 187272009150 active site 187272009151 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 187272009152 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 187272009153 putative ribose interaction site [chemical binding]; other site 187272009154 putative ADP binding site [chemical binding]; other site 187272009155 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 187272009156 active site 187272009157 HIGH motif; other site 187272009158 nucleotide binding site [chemical binding]; other site 187272009159 (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 187272009160 dimer interaction site [polypeptide binding]; other site 187272009161 substrate-binding tunnel; other site 187272009162 active site 187272009163 catalytic site [active] 187272009164 substrate binding site [chemical binding]; other site 187272009165 cobyric acid synthase; Provisional; Region: PRK00784 187272009166 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 187272009167 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 187272009168 catalytic triad [active] 187272009169 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 187272009170 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 187272009171 DEC-1 protein, N-terminal region; Region: DEC-1_N; pfam04625 187272009172 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 187272009173 catalytic triad [active] 187272009174 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 187272009175 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; Region: CobA_CobO_BtuR; cl17276 187272009176 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 187272009177 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 187272009178 N-terminal plug; other site 187272009179 ligand-binding site [chemical binding]; other site 187272009180 cobalamin synthase; Reviewed; Region: cobS; PRK00235 187272009181 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 187272009182 catalytic core [active] 187272009183 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 187272009184 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 187272009185 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 187272009186 pyridoxal 5'-phosphate binding site [chemical binding]; other site 187272009187 homodimer interface [polypeptide binding]; other site 187272009188 catalytic residue [active] 187272009189 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 187272009190 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 187272009191 cobalamin binding residues [chemical binding]; other site 187272009192 putative BtuC binding residues; other site 187272009193 dimer interface [polypeptide binding]; other site 187272009194 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 187272009195 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 187272009196 ABC-ATPase subunit interface; other site 187272009197 dimer interface [polypeptide binding]; other site 187272009198 putative PBP binding regions; other site 187272009199 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 187272009200 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 187272009201 Walker A/P-loop; other site 187272009202 ATP binding site [chemical binding]; other site 187272009203 Q-loop/lid; other site 187272009204 ABC transporter signature motif; other site 187272009205 Walker B; other site 187272009206 D-loop; other site 187272009207 H-loop/switch region; other site 187272009208 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 187272009209 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 187272009210 putative dimer interface [polypeptide binding]; other site 187272009211 active site pocket [active] 187272009212 putative cataytic base [active] 187272009213 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 187272009214 homotrimer interface [polypeptide binding]; other site 187272009215 Walker A motif; other site 187272009216 GTP binding site [chemical binding]; other site 187272009217 Walker B motif; other site 187272009218 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 187272009219 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 187272009220 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 187272009221 shikimate binding site; other site 187272009222 NAD(P) binding site [chemical binding]; other site 187272009223 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 187272009224 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 187272009225 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 187272009226 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 187272009227 dimer interface [polypeptide binding]; other site 187272009228 allosteric magnesium binding site [ion binding]; other site 187272009229 active site 187272009230 aspartate-rich active site metal binding site; other site 187272009231 Schiff base residues; other site 187272009232 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 187272009233 hypothetical protein; Validated; Region: PRK09039 187272009234 FlxA-like protein; Region: FlxA; pfam14282 187272009235 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 187272009236 ligand binding site [chemical binding]; other site 187272009237 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 187272009238 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 187272009239 Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to...; Region: PRK_like; cd02029 187272009240 active site 187272009241 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 187272009242 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 187272009243 substrate binding site [chemical binding]; other site 187272009244 hexamer interface [polypeptide binding]; other site 187272009245 metal binding site [ion binding]; metal-binding site 187272009246 Transcriptional regulator [Transcription]; Region: LysR; COG0583 187272009247 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272009248 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 187272009249 putative dimerization interface [polypeptide binding]; other site 187272009250 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 187272009251 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 187272009252 dimer interface [polypeptide binding]; other site 187272009253 catalytic residue [active] 187272009254 metal binding site [ion binding]; metal-binding site 187272009255 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 187272009256 multimerization interface [polypeptide binding]; other site 187272009257 MoxR-like ATPases [General function prediction only]; Region: COG0714 187272009258 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 187272009259 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 187272009260 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 187272009261 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 187272009262 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 187272009263 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 187272009264 transketolase; Reviewed; Region: PRK12753 187272009265 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 187272009266 TPP-binding site [chemical binding]; other site 187272009267 dimer interface [polypeptide binding]; other site 187272009268 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 187272009269 PYR/PP interface [polypeptide binding]; other site 187272009270 dimer interface [polypeptide binding]; other site 187272009271 TPP binding site [chemical binding]; other site 187272009272 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 187272009273 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 187272009274 Phosphoglycerate kinase; Region: PGK; pfam00162 187272009275 substrate binding site [chemical binding]; other site 187272009276 hinge regions; other site 187272009277 ADP binding site [chemical binding]; other site 187272009278 catalytic site [active] 187272009279 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 187272009280 pyruvate kinase; Provisional; Region: PRK05826 187272009281 domain interfaces; other site 187272009282 active site 187272009283 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 187272009284 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 187272009285 intersubunit interface [polypeptide binding]; other site 187272009286 active site 187272009287 zinc binding site [ion binding]; other site 187272009288 Na+ binding site [ion binding]; other site 187272009289 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 187272009290 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 187272009291 active site 187272009292 substrate binding site [chemical binding]; other site 187272009293 metal binding site [ion binding]; metal-binding site 187272009294 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 187272009295 trimer interface [polypeptide binding]; other site 187272009296 active site 187272009297 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 187272009298 Flavoprotein; Region: Flavoprotein; pfam02441 187272009299 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 187272009300 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 187272009301 Na2 binding site [ion binding]; other site 187272009302 putative substrate binding site 1 [chemical binding]; other site 187272009303 Na binding site 1 [ion binding]; other site 187272009304 putative substrate binding site 2 [chemical binding]; other site 187272009305 putative catalytic site [active] 187272009306 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 187272009307 putative metal binding site [ion binding]; other site 187272009308 putative phosphate binding site [ion binding]; other site 187272009309 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 187272009310 catalytic residues [active] 187272009311 hinge region; other site 187272009312 alpha helical domain; other site 187272009313 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 187272009314 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 187272009315 ResB-like family; Region: ResB; pfam05140 187272009316 ResB-like family; Region: ResB; pfam05140 187272009317 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 187272009318 Cytochrome c553 [Energy production and conversion]; Region: COG2863 187272009319 Cytochrome c; Region: Cytochrom_C; cl11414 187272009320 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 187272009321 TMAO/DMSO reductase; Reviewed; Region: PRK05363 187272009322 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 187272009323 Moco binding site; other site 187272009324 metal coordination site [ion binding]; other site 187272009325 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 187272009326 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 187272009327 G1 box; other site 187272009328 GTP/Mg2+ binding site [chemical binding]; other site 187272009329 Switch I region; other site 187272009330 G2 box; other site 187272009331 G3 box; other site 187272009332 Switch II region; other site 187272009333 G4 box; other site 187272009334 G5 box; other site 187272009335 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 187272009336 DNA polymerase I; Provisional; Region: PRK05755 187272009337 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 187272009338 active site 187272009339 metal binding site 1 [ion binding]; metal-binding site 187272009340 putative 5' ssDNA interaction site; other site 187272009341 metal binding site 3; metal-binding site 187272009342 metal binding site 2 [ion binding]; metal-binding site 187272009343 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 187272009344 putative DNA binding site [nucleotide binding]; other site 187272009345 putative metal binding site [ion binding]; other site 187272009346 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 187272009347 active site 187272009348 catalytic site [active] 187272009349 substrate binding site [chemical binding]; other site 187272009350 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 187272009351 active site 187272009352 DNA binding site [nucleotide binding] 187272009353 catalytic site [active] 187272009354 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 187272009355 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 187272009356 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 187272009357 Part of AAA domain; Region: AAA_19; pfam13245 187272009358 Protein of unknown function DUF54; Region: DUF54; cl00585 187272009359 Family description; Region: UvrD_C_2; pfam13538 187272009360 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 187272009361 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 187272009362 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 187272009363 dimerization interface [polypeptide binding]; other site 187272009364 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 187272009365 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 187272009366 glutaminase active site [active] 187272009367 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 187272009368 dimer interface [polypeptide binding]; other site 187272009369 active site 187272009370 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 187272009371 dimer interface [polypeptide binding]; other site 187272009372 active site 187272009373 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 187272009374 Ligand Binding Site [chemical binding]; other site 187272009375 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 187272009376 Ligand Binding Site [chemical binding]; other site 187272009377 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 187272009378 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 187272009379 Substrate binding site; other site 187272009380 Mg++ binding site; other site 187272009381 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 187272009382 active site 187272009383 substrate binding site [chemical binding]; other site 187272009384 CoA binding site [chemical binding]; other site 187272009385 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 187272009386 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 187272009387 gamma subunit interface [polypeptide binding]; other site 187272009388 LBP interface [polypeptide binding]; other site 187272009389 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 187272009390 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 187272009391 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 187272009392 alpha subunit interaction interface [polypeptide binding]; other site 187272009393 Walker A motif; other site 187272009394 ATP binding site [chemical binding]; other site 187272009395 Walker B motif; other site 187272009396 inhibitor binding site; inhibition site 187272009397 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 187272009398 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 187272009399 core domain interface [polypeptide binding]; other site 187272009400 delta subunit interface [polypeptide binding]; other site 187272009401 epsilon subunit interface [polypeptide binding]; other site 187272009402 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 187272009403 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 187272009404 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 187272009405 beta subunit interaction interface [polypeptide binding]; other site 187272009406 Walker A motif; other site 187272009407 ATP binding site [chemical binding]; other site 187272009408 Walker B motif; other site 187272009409 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 187272009410 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 187272009411 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 187272009412 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 187272009413 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 187272009414 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 187272009415 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 187272009416 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 187272009417 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 187272009418 ParB-like nuclease domain; Region: ParBc; pfam02195 187272009419 KorB domain; Region: KorB; pfam08535 187272009420 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 187272009421 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 187272009422 P-loop; other site 187272009423 Magnesium ion binding site [ion binding]; other site 187272009424 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 187272009425 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 187272009426 S-adenosylmethionine binding site [chemical binding]; other site 187272009427 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 187272009428 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 187272009429 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 187272009430 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 187272009431 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 187272009432 trmE is a tRNA modification GTPase; Region: trmE; cd04164 187272009433 G1 box; other site 187272009434 GTP/Mg2+ binding site [chemical binding]; other site 187272009435 Switch I region; other site 187272009436 G2 box; other site 187272009437 Switch II region; other site 187272009438 G3 box; other site 187272009439 G4 box; other site 187272009440 G5 box; other site 187272009441 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 187272009442 membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Region: yidC_nterm; TIGR03593 187272009443 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 187272009444 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 187272009445 Ribonuclease P; Region: Ribonuclease_P; pfam00825 187272009446 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399